Error: program build failure (-11) occurs when running NextGenMap with Docker

[penguinmeow]

Hi there~ I wanna report an Error occurs when try to run NGM with Docker. While it can be ran through smoothly with NextGenMap installed in PC. Thank you so much!

(base) xzhen@L190514  ~/Documents/SLAM  docker run -m 8g -v $(pwd):/data -ti philres/nextgenmap ngm -r /data/dh10b_ecoli.fasta -1 /data/dh10b_ecoli.fasta_1.fastq -2 /data/dh10b_ecoli.fasta_2.fastq -o /data/dh10b_ecoli.fasta_mapped_ngm.sam

[MAIN] NextGenMap 0.5.5 [MAIN] Startup : x64 (build Jul 22 2018 20:40:59) [MAIN] Starting time: 2020-11-04.23:22:27 [CONFIG] Parameter: --affine 0 --argos_min_score 0 --bin_size 2 --block_multiplier 2 --broken_pairs 0 --bs_cutoff 6 --bs_mapping 0 --cpu_threads 1 --dualstrand 1 --fast 0 --fast_pairing 0 --force_rlength_check 0 --format 1 --gap_extend_penalty 5 --gap_read_penalty 20 --gap_ref_penalty 20 --hard_clip 0 --keep_tags 0 --kmer 13 --kmer_min 0 --kmer_skip 2 --match_bonus 10 --match_bonus_tc 2 --match_bonus_tt 10 --max_cmrs 2147483647 --max_equal 1 --max_insert_size 1000 --max_polya -1 --max_read_length 0 --min_identity 0.650000 --min_insert_size 0 --min_mq 0 --min_residues 0.500000 --min_score 0.000000 --mismatch_penalty 15 --mode 0 --no_progress 0 --no_unal 0 --ocl_threads 1 --output /data/dh10b_ecoli.fasta_mapped_ngm.sam --overwrite 1 --pair_score_cutoff 0.900000 --paired 1 --parse_all 1 --pe_delimiter / --qry1 /data/dh10b_ecoli.fasta_1.fastq --qry2 /data/dh10b_ecoli.fasta_2.fastq --qry_count -1 --qry_start 0 --ref /data/dh10b_ecoli.fasta --ref_mode -1 --sensitive 0 --silent_clip 0 --skip_mate_check 0 --skip_save 0 --slam_seq 0 --step_count 4 --strata 0 --topn 1 --trim5 0 --update_check 0 --very_fast 0 --very_sensitive 0 [NGM] Opening for output (SAM): /data/dh10b_ecoli.fasta_mapped_ngm.sam [SEQPROV] Reading encoded reference from /data/dh10b_ecoli.fasta-enc.2.ngm [SEQPROV] Reading 4 Mbp from disk took 0.02s [PREPROCESS] Reading RefTable from /data/dh10b_ecoli.fasta-ht-13-2.3.ngm [PREPROCESS] Reading from disk took 2.58s [PREPROCESS] Max. k-mer frequency set so 100! [INPUT] Input is paired end data. [INPUT] Opening file /data/dh10b_ecoli.fasta_1.fastq for reading [INPUT] Opening file /data/dh10b_ecoli.fasta_2.fastq for reading [INPUT] Input is Fastq [INPUT] Estimating parameter from data [INPUT] Reads found in files: 1000 [INPUT] Average read length: 100 (min: 100, max: 102) [INPUT] Corridor width: 20 [INPUT] Average kmer hits pro read: 29.000000 [INPUT] Max possible kmer hit: 29 [INPUT] Estimated sensitivity: 0.900000 [INPUT] Estimating parameter took 0.011s [INPUT] Input is Fastq [INPUT] Input is Fastq [OPENCL] Available platforms: 1 [OPENCL] AMD Accelerated Parallel Processing [OPENCL] Selecting OpenCl platform: AMD Accelerated Parallel Processing [OPENCL] Platform: OpenCL 1.2 AMD-APP (1214.3) [OPENCL] 1 CPU device found. [OPENCL] Device 0: Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz (Driver: 1214.3 (sse2,avx)) [OPENCL] 6 CPU cores available. [Progress] Mapped: 1, CMR/R: 0, CS: 0 (0), R/S: 0, Time: 0.00 0.00 0.00, Pa[Progress] Mapped: 1, CMR/R: 0, CS: 0 (0), R/S: 0, Time: 0.00 0.00 0.00, Pa[Progress] Mapped: 1, CMR/R: 0, CS: 0 (0), R/S: 0, Time: 0.00 0.00 0.00, Pa[OPENCL] Build failed: Program build failure [OPENCL] Build status: build failed [OPENCL] Build log: [OPENCL] Internal Error: as failed [OPENCL] Codegen phase failed compilation. [OPENCL] Unable to build program end. Error: Program build failure (-11) terminate called without an active exception

[fritzsedlazeck]

It looks like a problem wiht the GPU drivers (OpenCL) to me. Maybe there is an issue with libaries ? Thanks Fritz

[didillysquat]

Same issue here using docker within a nextflow pipeline:

Error executing process > 'nextgenmap (null)'

Caused by: Process nextgenmap (null) terminated with an error exit status (134)

Command executed:

ngm -t 40 -r /home/humebc/projects/20210125_kopp_guinea_fowl/nf_pipeline_kopp/nummel_ref_assembly/GCF_002078875.1_NumMel1.0_genomic.fna.gz -1 mpg_L16994-1_W1393_S70_sub_10000_R1_001.trimmed_1P.fq.gz -2 mpg_L16994-1_W1393_S70_sub_10000_R1_001.trimmed_2P.fq.gz -o mpg_L16994-1_W1393_S70_sub_10000_paired_mapped.sam; ngm -t 40 -r /home/humebc/projects/20210125_kopp_guinea_fowl/nf_pipeline_kopp/nummel_ref_assembly/GCF_002078875.1_NumMel1.0_genomic.fna.gz -q mpg_L16994-1_W1393_S70_sub_10000_R1_001.trimmed_1U.fq.gz -o mpg_L16994-1_W1393_S70_sub_10000_U1_mapped.sam; ngm -t 40 -r ./home/humebc/projects/20210125_kopp_guinea_fowl/nf_pipeline_kopp/nummel_ref_assembly/GCF_002078875.1_NumMel1.0_genomic.fna.gz -q mpg_L16994-1_W1393_S70_sub_10000_R1_001.trimmed_2U.fq.gz -o mpg_L16994-1_W1393_S70_sub_10000_U2_unpaired.sam;

Command exit status: 134

Command output: (empty)

Command error: [SEQPROV] Reading 1045 Mbp from disk took 0.27s [PREPROCESS] Building reference table [PREPROCESS] Allocated 1 hashtable units (tableLocMax=2^32.000000, genomeSize=2^29.961867) [PREPROCESS] Building RefTable #0 (kmer length: 13, reference skip: 2) [PREPROCESS] Number of k-mers: 67108865 [PREPROCESS] Counting kmers took 26.08s [PREPROCESS] lAverage number of positions per prefix: 7.060357 [PREPROCESS] AIndex size: 335544325 byte (67108865 x 5) [PREPROCESS] cGenerating index took 3.20s [PREPROCESS] fAllocating and initializing prefix Table took 0.41s [PREPROCESS] UNumber of prefix positions is 340968351 (4) [PREPROCESS] cSize of RefTable is 1363873404 [PREPROCESS] CNumber of repetitive k-mers ignored: 12657 [PREPROCESS] dOverall time for creating RefTable: 139.72s [PREPROCESS] Writing RefTable to /home/humebc/projects/20210125_kopp_guinea_fowl/nf_pipeline_kopp/nummel_ref_assembly/GCF_002078875.1_NumMel1.0_genomic.fna.gz-ht-13-2.3.ngm [PREPROCESS] Writing to disk took 3.20s [PREPROCESS] Max. k-mer frequency set so 100! [INPUT] Input is paired end data. [INPUT] Opening file mpg_L16994-1_W1393_S70_sub_10000_R1_001.trimmed_1P.fq.gz for reading [INPUT] Opening file mpg_L16994-1_W1393_S70_sub_10000_R1_001.trimmed_2P.fq.gz for reading [INPUT] Input is Fastq [INPUT] Estimating parameter from data [INPUT] Reads found in files: 7901 [INPUT] Average read length: 142 (min: 65, max: 146) [INPUT] Corridor width: 26 [INPUT] Average kmer hits pro read: 21.264109 [INPUT] Max possible kmer hit: 43 [INPUT] Estimated sensitivity: 0.494514 [INPUT] Estimating parameter took 0.024s [INPUT] Input is Fastq [INPUT] Input is Fastq [OPENCL] Available platforms: 1 [OPENCL] AMD Accelerated Parallel Processing [OPENCL] Selecting OpenCl platform: AMD Accelerated Parallel Processing [OPENCL] Platform: OpenCL 1.2 AMD-APP (1214.3) [OPENCL] 1 CPU device found. [OPENCL] Device 0: AMD EPYC 7702 64-Core Processor (Driver: 1214.3 (sse2,avx)) [OPENCL] 256 CPU cores available. [OPENCL] Build failed: Program build failure [OPENCL] Build status: build failed [OPENCL] Build log: [OPENCL] Internal Error: as failed [OPENCL] Codegen phase failed compilation. [OPENCL] Unable to build program end. Error: Program build failure (-11) terminate called without an active exception .command.sh: line 2: 8 Aborted (core dumped) ngm -t 40 -r /home/humebc/projects/20210125_kopp_guinea_fowl/nf_pipeline_kopp/nummel_ref_assembly/GCF_002078875.1_NumMel1.0_genomic.fna.gz -1 mpg_L16994-1_W1393_S70_sub_10000_R1_001.trimmed_1P.fq.gz -2 mpg_L16994-1_W1393_S70_sub_10000_R1_001.trimmed_2P.fq.gz -o mpg_L16994-1_W1393_S70_sub_10000_paired_mapped.sam

Work dir: /home/humebc/projects/20210125_kopp_guinea_fowl/nf_pipeline_kopp/work/93/67eb25eb111b665acb919e37adfc51

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run