salmon
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COMBINE-lab
salmon quant was invoked improperly. For usage information, try salmon quant --help Exiting.
Hi there,
here is my error and i ll provide my script
Version Info: This is the most recent version of salmon.
salmon (selective-alignment-based) v1.10.1
[ program ] => salmon
[ command ] => quant
[ index ] => { salmon_index }
[ libType ] => { A }
[ mates1 ] => { /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_33-41/33-41_221020_L002_R1.fastq.gz
/nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_32-40/32-40_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_38-45_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_30-38/30-38_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_20-28/20-28_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_13-21/13-21_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-6-12_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_17-25/17-25_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-11-18_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_7-14/7-14_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_15-23_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_2-4/2-4_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_35-43/35-43_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_18-26_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_41-49_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_48-56/48-56_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-10-17_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_43-52_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-5-11_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_26-34_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_24-32_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_21-29_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_28-36/28-36_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_9-16/9-16_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-44-51_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_47-55/47-55_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_29-37/29-37_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_12-20/12-20_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_34-42/34-42_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_36-44_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_40-48_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_1_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_19-27_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_31-39/31-39_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_3-6/3-6_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_14-22/14-22_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_37-46_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_39-47_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_8-15/8-15_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_42-50_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-46-53_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-4-10_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_23-31/23-31_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_16-24_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_22-30/22-30_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_27-35/27-35_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_25-33/25-33_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-45-54_221020_L002_R1.fastq.gz }
[ mates2 ] => { /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_36-44_221020_L002_R2.fastq.gz
/nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_33-41/33-41_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_24-32_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_19-27_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-46-53_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_32-40/32-40_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_41-49_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_30-38/30-38_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_20-28/20-28_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_13-21/13-21_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-10-17_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_17-25/17-25_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_7-14/7-14_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_2-4/2-4_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_35-43/35-43_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_37-46_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-44-51_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_1_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_48-56/48-56_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_15-23_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-6-12_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_26-34_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_28-36/28-36_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_42-50_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_9-16/9-16_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_21-29_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_40-48_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-11-18_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_47-55/47-55_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_29-37/29-37_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_12-20/12-20_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_34-42/34-42_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_18-26_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_16-24_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_31-39/31-39_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-4-10_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_3-6/3-6_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_14-22/14-22_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_38-45_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_8-15/8-15_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_23-31/23-31_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_43-52_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-45-54_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_39-47_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_22-30/22-30_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_27-35/27-35_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_25-33/25-33_221020_L002_R2.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-5-11_221020_L002_R2.fastq.gz }
[ threads ] => { 100 }
[ validateMappings ] => { }
[ output ] => { salmon_out/P2-45-54_221020_L002_R1.fastq.gz_quant }
Logs will be written to salmon_out/P2-45-54_221020_L002_R1.fastq.gz_quant/logs [2023-08-27 19:59:26.866] [jointLog] [info] setting maxHashResizeThreads to 100 [2023-08-27 19:59:26.866] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2023-08-27 19:59:26.866] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2023-08-27 19:59:26.866] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35. [2023-08-27 19:59:26.866] [jointLog] [info] parsing read library format [2023-08-27 19:59:26.866] [jointLog] [info] There is 1 library. [2023-08-27 19:59:26.867] [jointLog] [info] Loading pufferfish index [2023-08-27 19:59:26.867] [jointLog] [info] Loading dense pufferfish index.
| Loading contig table | Time = 3.5071 s
size = 23930024
| Loading contig offsets | Time = 66.098 ms
| Loading reference lengths | Time = 15.687 ms
| Loading mphf table | Time = 157.98 ms
size = 2092742871 Number of ones: 23930023 Number of ones per inventory item: 512 Inventory entries filled: 46739
| Loading contig boundaries | Time = 2.8293 s
size = 2092742871
| Loading sequence | Time = 394.6 ms
size = 1374842181
| Loading positions | Time = 4.3258 s
size = 2139249936
| Loading reference sequence | Time = 408.65 ms
| Loading reference accumulative lengths | Time = 48.085 ms
Exception : [boost::filesystem::status: File name too long: "/nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_33-41/33-41_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_32-40/32-40_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_38-45_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_30-38/30-38_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_20-28/20-28_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_13-21/13-21_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-6-12_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_17-25/17-25_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-11-18_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_7-14/7-14_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_15-23_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_2-4/2-4_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_35-43/35-43_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_18-26_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_41-49_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_48-56/48-56_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-10-17_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_43-52_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-5-11_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_26-34_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_24-32_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_21-29_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_28-36/28-36_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_9-16/9-16_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-44-51_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_47-55/47-55_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_29-37/29-37_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_12-20/12-20_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_34-42/34-42_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_36-44_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_40-48_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_1_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_19-27_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_31-39/31-39_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_3-6/3-6_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_14-22/14-22_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_37-46_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_39-47_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_8-15/8-15_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P3_42-50_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-46-53_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-4-10_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_23-31/23-31_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P1_H.m_16-24_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_22-30/22-30_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_27-35/27-35_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/Sample_25-33/25-33_221020_L002_R1.fastq.gz /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/P2-45-54_221020_L002_R1.fastq.gz"] salmon quant was invoked improperly. For usage information, try salmon quant --help Exiting.
script
#!/bin/bash #SBATCH -p shared #SBATCH -c 100 #SBATCH --mem=200G #SBATCH --gres=tmp:300G #SBATCH -t 36:00:00
module purge module load bioinformatics module load salmon/1.10.1
cd /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/
Set the path to the Salmon index
salmon_index="/nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/salmon_index"
Set the path to the directory containing all the FASTQ files
fastq_dir="/nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed"
Use the find command to locate all R1 and R2 FASTQ files
r1_files=$(find "$fastq_dir" -name "*1.fastq.gz") r2_files=$(find "$fastq_dir" -name "*2.fastq.gz")
Loop through the found files
for i in "${!r1_files[@]}"; do r1_file="${r1_files[i]}" r2_file="${r2_files[i]}"
# Extract the sample name
samp=$(basename "$r1_file" "_1.fastq.gz")
echo "Processing sample ${samp}"
salmon quant -i salmon_index -l A -1 "$r1_file" -2 "$r2_file" -p 100 --validateMappings -o "salmon_out/${samp}_quant"
done
thanks
Hi @Alecrim24,
It looks like the list of r1 files are being interpreted as a single, long, filename. Same with the list of r2 files. Any idea why that's the case? They should be a space-separated list (of course, there are a ton of them here, but the error clearly suggests they are being interpreted as a single, long, filename).
--Rob
Hi rob
Ignore my last email
I did it again using this script
#!/bin/bash #SBATCH -p shared #SBATCH -c 100 #SBATCH --mem=200G #SBATCH --gres=tmp:300G #SBATCH -t 36:00:00
module purge module load bioinformatics module load salmon/1.10.1
cd /nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/
Set the path to the Salmon index
salmon_index="/nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed/salmon_index"
Set the path to the directory containing all the FASTQ files
fastq_dir="/nobackup/qkdf72/Trinity/Reads/All-H.m-reads/Trimmed"
Create an array of left and right read files
left_files=( P1_H.m_1_221020_L002_R1.fastq.gz P1_H.m_21-29_221020_L002_R1.fastq.gz P2-4-10_221020_L002_R1.fastq.gz P2-6-12_221020_L002_R1.fastq.gz P3_40-48_221020_L002_R1.fastq.gz P1_H.m_15-23_221020_L002_R1.fastq.gz P1_H.m_24-32_221020_L002_R1.fastq.gz P2-44-51_221020_L002_R1.fastq.gz P3_36-44_221020_L002_R1.fastq.gz P3_41-49_221020_L002_R1.fastq.gz P1_H.m_16-24_221020_L002_R1.fastq.gz P1_H.m_26-34_221020_L002_R1.fastq.gz P2-45-54_221020_L002_R1.fastq.gz P3_37-46_221020_L002_R1.fastq.gz P3_42-50_221020_L002_R1.fastq.gz P1_H.m_18-26_221020_L002_R1.fastq.gz P2-10-17_221020_L002_R1.fastq.gz P2-46-53_221020_L002_R1.fastq.gz P3_38-45_221020_L002_R1.fastq.gz P3_43-52_221020_L002_R1.fastq.gz P1_H.m_19-27_221020_L002_R1.fastq.gz P2-11-18_221020_L002_R1.fastq.gz P2-5-11_221020_L002_R1.fastq.gz P3_39-47_221020_L002_R1.fastq.gz )
right_files=( P1_H.m_1_221020_L002_R2.fastq.gz P1_H.m_21-29_221020_L002_R2.fastq.gz P2-4-10_221020_L002_R2.fastq.gz P2-6-12_221020_L002_R2.fastq.gz P3_40-48_221020_L002_R2.fastq.gz P1_H.m_15-23_221020_L002_R2.fastq.gz P1_H.m_24-32_221020_L002_R2.fastq.gz P2-44-51_221020_L002_R2.fastq.gz P3_36-44_221020_L002_R2.fastq.gz P3_41-49_221020_L002_R2.fastq.gz P1_H.m_16-24_221020_L002_R2.fastq.gz P1_H.m_26-34_221020_L002_R2.fastq.gz P2-45-54_221020_L002_R2.fastq.gz P3_37-46_221020_L002_R2.fastq.gz P3_42-50_221020_L002_R2.fastq.gz P1_H.m_18-26_221020_L002_R2.fastq.gz P2-10-17_221020_L002_R2.fastq.gz P2-46-53_221020_L002_R2.fastq.gz P3_38-45_221020_L002_R2.fastq.gz P3_43-52_221020_L002_R2.fastq.gz P1_H.m_19-27_221020_L002_R2.fastq.gz P2-11-18_221020_L002_R2.fastq.gz P2-5-11_221020_L002_R2.fastq.gz P3_39-47_221020_L002_R2.fastq.gz
)
Loop through the read files and run Salmon quant
for i in "${!left_files[@]}"; do left_file="${left_files[i]}" right_file="${right_files[i]}"
# Extract the sample name
sample=$(basename "$left_file" "_L002_R1.fastq.gz")
# Run Salmon quant with the current read files
salmon quant -i "$salmon_index" -l IU -1 "$fastq_dir/$left_file" -2 "$fastq_dir/$right_file" --validateMappings -o "salmon_out/${sample}_quant"
done
and the results of the first 2 look like this
Name Length EffectiveLength TPM NumReads TRINITY_DN1448606_c0_g1_i1 472 275.399 0.000000 0.000 TRINITY_DN1448584_c0_g1_i1 394 201.561 0.000000 0.000 TRINITY_DN1448585_c0_g1_i2 237 72.382 0.000000 0.000 TRINITY_DN1448598_c0_g1_i1 227 65.738 0.000000 0.000 TRINITY_DN1448598_c1_g1_i1 254 84.301 0.000000 0.000 TRINITY_DN1448554_c0_g1_i1 349 160.724 0.000000 0.000 TRINITY_DN1448554_c1_g1_i1 247 79.278 0.000000 0.000 TRINITY_DN1448554_c2_g1_i1 242 75.824 0.000000 0.000 TRINITY_DN1448616_c0_g1_i1 313 129.689 0.000000 0.000 [[email protected] P1_H.m_1_221020_quant]$ cd .. [[email protected] salmon_out]$ cd P1_H.m_21-29_221020_quant/ [[email protected] P1_H.m_21-29_221020_quant]$ head quant.sf Name Length EffectiveLength TPM NumReads TRINITY_DN1448606_c0_g1_i1 472 298.999 0.000000 0.000 TRINITY_DN1448584_c0_g1_i1 394 222.370 0.000000 0.000 TRINITY_DN1448585_c0_g1_i2 237 75.234 0.000000 0.000 TRINITY_DN1448598_c0_g1_i1 227 66.771 0.000000 0.000 TRINITY_DN1448598_c1_g1_i1 254 90.379 0.000000 0.000 TRINITY_DN1448554_c0_g1_i1 349 178.865 0.000000 0.000 TRINITY_DN1448554_c1_g1_i1 247 84.098 0.000000 0.000 TRINITY_DN1448554_c2_g1_i1 242 79.642 0.000000 0.000 TRINITY_DN1448616_c0_g1_i1 313 144.704 0.000000 0.000
AS you can see the name and the length are the same for both but the others vary.
Is this right?
kind regards