continuation from #924, warnings.warn("fragmentSize.metric.tsv is empty, this sets

[sunta3iouxos]

This is the error I encountered:

ChIP-seq -d /mnt/c/AP01/bamSpikes -j 8 --local --useSpikeInForNorm --getSizeFactorsFrom genome --spikeinExt Chromosome --sampleSheet /mnt/c/AP01/bamSpikes/H3K36me3.tsv --windowSize 500 mm10_gencodeM19_spikes /mnt/c/AP01/bamSpikes/H3K36me3_chip_type.yaml

mambaforge/envs/snakePipes/lib/python3.11/site-packages/snakePipes/workflows/ChIP-seq/internals.snakefile:71: UserWarning: fragmentSize.metric.tsv is empty, this sets --extsize of MACS2 to an empty string. Fix this and run MACS2 again!
  warnings.warn("fragmentSize.metric.tsv is empty, this sets "

but the file as expected is there and is not empty. Maybe I need to change the path of "filtered_bam/A006200317_201074_S18_L000.filtered.bam"?

this is the entry in **fragmentSize.metric.tsv** in folder /mnt/c/AP01/bamSpikes/deepTools_qc/bamPEFragmentSize

Frag. Sampled	Frag. Len. Min.	Frag. Len. 1st. Qu.	Frag. Len. Mean	Frag. Len. Median	Frag. Len. 3rd Qu.	Frag. Len. Max	Frag. Len. Std.	Frag. Med. Abs. Dev.	Frag. Len. 10%	Frag. Len. 20%	Frag. Len. 30%	Frag. Len. 40%	Frag. Len. 60%	Frag. Len. 70%	Frag. Len. 80%	Frag. Len. 90%	Frag. Len. 99%	Reads Sampled	Read Len. Min.	Read Len. 1st. Qu.	Read Len. Mean	Read Len. Median	Read Len. 3rd Qu.	Read Len. Max	Read Len. Std.	Read Med. Abs. Dev.	Read Len. 10%	Read Len. 20%	Read Len. 30%	Read Len. 40%	Read Len. 60%	Read Len. 70%	Read Len. 80%	Read Len. 90%	Read Len. 99%
filtered_bam/A006200317_201074_S18_L000.filtered.bam	5161291	31.0	232.0	383.59622621549534	347.0	503.0	1000.0	180.41123400583055	134.0	174.0	204.0	279.0	324.0	375.0	462.0	535.0	660.0	879.0	5161291	6.0	101.0	100.82193892962052	101.0	101.0	101.0	2.2590399841527473	0.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0
filtered_bam/A006200317_201076_S19_L000.filtered.bam	4998218	31.0	244.0	388.9016327419092	350.0	508.0	1000.0	181.67450743477957	133.0	175.0	210.0	289.0	326.0	381.0	471.0	540.0	666.0	885.0	4998218	5.0	101.0	100.8087454368737	101.0	101.0	101.0	2.36251289170861	0.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0
filtered_bam/A006200317_201078_S20_L000.filtered.bam	4842611	31.0	234.0	377.8803847758988	343.0	491.0	1000.0	176.66208868323568	126.0	175.0	206.0	275.0	319.0	370.0	444.0	525.0	646.0	875.0	4842611	6.0	101.0	100.79993437424562	101.0	101.0	101.0	2.450860570721792	0.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0
filtered_bam/A006200317_201080_S21_L000.filtered.bam	4231126	31.0	215.0	363.7680144717978	336.0	467.0	1000.0	172.56381732262406	124.0	172.0	196.0	244.0	309.0	361.0	408.0	509.0	617.0	864.0	4231126	9.0	101.0	100.84629339802218	101.0	101.0	101.0	2.0855938850499705	0.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0
filtered_bam/A006200317_201082_S22_L000.filtered.bam	4603157	30.0	231.0	381.17343032184215	343.0	498.0	1000.0	181.16802233137997	130.0	174.0	205.0	267.0	316.0	376.0	457.0	533.0	657.0	880.0	4603157	6.0	101.0	100.8004684611018	101.0	101.0	101.0	2.440956246140944	0.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0
filtered_bam/A006200317_201084_S23_L000.filtered.bam	5281531	0.0	197.0	357.5763482217562	333.0	474.0	16124.0	176.92660091806692	137.0	166.0	184.0	215.0	300.0	358.0	409.0	513.0	622.0	849.0	5281531	4.0	101.0	100.8138689330802	101.0	101.0	101.0	2.2821954751618945	0.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0
filtered_bam/A006200317_201086_S24_L000.filtered.bam	4401065	31.0	212.0	374.26831914547955	351.0	483.0	1000.0	179.37549730915046	138.0	179.0	199.0	231.0	325.0	373.0	406.0	534.0	637.0	890.0	4401065	6.0	101.0	100.82557017449186	101.0	101.0	101.0	2.301871383600218	0.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0
filtered_bam/A006200317_201088_S25_L000.filtered.bam	3847192	0.0	207.0	365.88952487944454	346.0	452.0	16170.0	177.7775288643752	136.0	176.0	196.0	222.0	315.0	368.0	398.0	524.0	616.0	883.0	3847192	5.0	101.0	100.81410103784786	101.0	101.0	101.0	2.40888097693432	0.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0
filtered_bam/A006200317_201090_S26_L000.filtered.bam	4093720	31.0	232.0	389.4095922535005	361.0	512.0	1000.0	178.40632084526274	137.0	183.0	210.0	289.0	339.0	382.0	433.0	546.0	656.0	892.0	4093720	7.0	101.0	100.81159629872097	101.0	101.0	101.0	2.4316634404585766	0.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0
filtered_bam/A006200317_201092_S27_L000.filtered.bam	3741218	0.0	231.0	381.22604536811275	355.0	487.0	1000.0	171.89024706022872	126.0	182.0	209.0	298.0	335.0	375.0	409.0	532.0	626.0	876.0	3741218	7.0	101.0	100.82066749384826	101.0	101.0	101.0	2.336261347282812	0.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0
filtered_bam/A006200317_201094_S28_L000.filtered.bam	3698962	31.0	258.0	381.6722956332074	355.0	475.0	1000.0	166.62108808100896	107.0	184.0	218.0	307.0	336.0	375.0	408.0	525.0	612.0	871.0	3698962	7.0	101.0	100.80471115950907	101.0	101.0	101.0	2.4712627909165152	0.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0
filtered_bam/A006200317_201096_S29_L000.filtered.bam	3480613	30.0	229.0	381.9273995701332	358.0	491.0	1000.0	171.77850031757265	130.0	184.0	209.0	289.0	337.0	377.0	413.0	535.0	620.0	874.0	3480613	6.0	101.0	100.8180673921519	101.0	101.0	101.0	2.3709500630069402	0.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0	101.0