Job ID = 12265118 SRX = SRX3088406 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:01 22416 reads; of these: 22416 (100.00%) were unpaired; of these: 14738 (65.75%) aligned 0 times 6483 (28.92%) aligned exactly 1 time 1195 (5.33%) aligned >1 times 34.25% overall alignment rate Time searching: 00:00:01 Overall time: 00:00:01 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 2733 / 7678 = 0.3560 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:09:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 03 Apr 2021 06:09:14: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:09:14: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:09:14: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:09:14: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:09:14: #1 total tags in treatment: 4945 INFO @ Sat, 03 Apr 2021 06:09:14: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:09:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:09:14: #1 tags after filtering in treatment: 4827 INFO @ Sat, 03 Apr 2021 06:09:14: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 03 Apr 2021 06:09:14: #1 finished! INFO @ Sat, 03 Apr 2021 06:09:14: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:09:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:09:14: #2 number of paired peaks: 159 WARNING @ Sat, 03 Apr 2021 06:09:14: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Sat, 03 Apr 2021 06:09:14: start model_add_line... INFO @ Sat, 03 Apr 2021 06:09:14: start X-correlation... INFO @ Sat, 03 Apr 2021 06:09:14: end of X-cor INFO @ Sat, 03 Apr 2021 06:09:14: #2 finished! INFO @ Sat, 03 Apr 2021 06:09:14: #2 predicted fragment length is 139 bps INFO @ Sat, 03 Apr 2021 06:09:14: #2 alternative fragment length(s) may be 8,34,54,81,102,139,154,187,231,262,284,321,353,413,464,511,536 bps INFO @ Sat, 03 Apr 2021 06:09:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.05_model.r WARNING @ Sat, 03 Apr 2021 06:09:14: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:09:14: #2 You may need to consider one of the other alternative d(s): 8,34,54,81,102,139,154,187,231,262,284,321,353,413,464,511,536 WARNING @ Sat, 03 Apr 2021 06:09:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:09:14: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:09:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:09:15: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:09:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:09:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:09:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.05_summits.bed INFO @ Sat, 03 Apr 2021 06:09:15: Done! pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:09:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 03 Apr 2021 06:09:44: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:09:44: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:09:44: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:09:44: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:09:44: #1 total tags in treatment: 4945 INFO @ Sat, 03 Apr 2021 06:09:44: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:09:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:09:44: #1 tags after filtering in treatment: 4827 INFO @ Sat, 03 Apr 2021 06:09:44: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 03 Apr 2021 06:09:44: #1 finished! INFO @ Sat, 03 Apr 2021 06:09:44: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:09:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:09:44: #2 number of paired peaks: 159 WARNING @ Sat, 03 Apr 2021 06:09:44: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Sat, 03 Apr 2021 06:09:44: start model_add_line... INFO @ Sat, 03 Apr 2021 06:09:44: start X-correlation... INFO @ Sat, 03 Apr 2021 06:09:44: end of X-cor INFO @ Sat, 03 Apr 2021 06:09:44: #2 finished! INFO @ Sat, 03 Apr 2021 06:09:44: #2 predicted fragment length is 139 bps INFO @ Sat, 03 Apr 2021 06:09:44: #2 alternative fragment length(s) may be 8,34,54,81,102,139,154,187,231,262,284,321,353,413,464,511,536 bps INFO @ Sat, 03 Apr 2021 06:09:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.10_model.r WARNING @ Sat, 03 Apr 2021 06:09:44: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:09:44: #2 You may need to consider one of the other alternative d(s): 8,34,54,81,102,139,154,187,231,262,284,321,353,413,464,511,536 WARNING @ Sat, 03 Apr 2021 06:09:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:09:44: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:09:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:09:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:09:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:09:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:09:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.10_summits.bed INFO @ Sat, 03 Apr 2021 06:09:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:10:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 03 Apr 2021 06:10:14: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:10:14: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:10:14: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:10:14: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:10:14: #1 total tags in treatment: 4945 INFO @ Sat, 03 Apr 2021 06:10:14: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:10:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:10:14: #1 tags after filtering in treatment: 4827 INFO @ Sat, 03 Apr 2021 06:10:14: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 03 Apr 2021 06:10:14: #1 finished! INFO @ Sat, 03 Apr 2021 06:10:14: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:10:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:10:14: #2 number of paired peaks: 159 WARNING @ Sat, 03 Apr 2021 06:10:14: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Sat, 03 Apr 2021 06:10:14: start model_add_line... INFO @ Sat, 03 Apr 2021 06:10:14: start X-correlation... INFO @ Sat, 03 Apr 2021 06:10:14: end of X-cor INFO @ Sat, 03 Apr 2021 06:10:14: #2 finished! INFO @ Sat, 03 Apr 2021 06:10:14: #2 predicted fragment length is 139 bps INFO @ Sat, 03 Apr 2021 06:10:14: #2 alternative fragment length(s) may be 8,34,54,81,102,139,154,187,231,262,284,321,353,413,464,511,536 bps INFO @ Sat, 03 Apr 2021 06:10:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.20_model.r WARNING @ Sat, 03 Apr 2021 06:10:14: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:10:14: #2 You may need to consider one of the other alternative d(s): 8,34,54,81,102,139,154,187,231,262,284,321,353,413,464,511,536 WARNING @ Sat, 03 Apr 2021 06:10:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:10:14: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:10:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:10:14: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:10:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:10:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:10:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3088406/SRX3088406.20_summits.bed INFO @ Sat, 03 Apr 2021 06:10:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling