Job ID = 10165771 SRX = SRX9120607 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 41837722 spots for SRR12638550/SRR12638550.sra Written 41837722 spots for SRR12638550/SRR12638550.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166090 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:15 41837722 reads; of these: 41837722 (100.00%) were unpaired; of these: 11197474 (26.76%) aligned 0 times 25172244 (60.17%) aligned exactly 1 time 5468004 (13.07%) aligned >1 times 73.24% overall alignment rate Time searching: 00:07:15 Overall time: 00:07:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 5983004 / 30640248 = 0.1953 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:06:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 08 Oct 2020 20:06:04: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:06:04: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:06:09: 1000000 INFO @ Thu, 08 Oct 2020 20:06:15: 2000000 INFO @ Thu, 08 Oct 2020 20:06:20: 3000000 INFO @ Thu, 08 Oct 2020 20:06:26: 4000000 INFO @ Thu, 08 Oct 2020 20:06:31: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:06:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 08 Oct 2020 20:06:35: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:06:35: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:06:37: 6000000 INFO @ Thu, 08 Oct 2020 20:06:41: 1000000 INFO @ Thu, 08 Oct 2020 20:06:44: 7000000 INFO @ Thu, 08 Oct 2020 20:06:47: 2000000 INFO @ Thu, 08 Oct 2020 20:06:50: 8000000 INFO @ Thu, 08 Oct 2020 20:06:53: 3000000 INFO @ Thu, 08 Oct 2020 20:06:56: 9000000 INFO @ Thu, 08 Oct 2020 20:06:59: 4000000 INFO @ Thu, 08 Oct 2020 20:07:02: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:07:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 08 Oct 2020 20:07:04: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:07:04: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:07:05: 5000000 INFO @ Thu, 08 Oct 2020 20:07:08: 11000000 INFO @ Thu, 08 Oct 2020 20:07:10: 1000000 INFO @ Thu, 08 Oct 2020 20:07:11: 6000000 INFO @ Thu, 08 Oct 2020 20:07:14: 12000000 INFO @ Thu, 08 Oct 2020 20:07:15: 2000000 INFO @ Thu, 08 Oct 2020 20:07:17: 7000000 INFO @ Thu, 08 Oct 2020 20:07:20: 13000000 INFO @ Thu, 08 Oct 2020 20:07:21: 3000000 INFO @ Thu, 08 Oct 2020 20:07:23: 8000000 INFO @ Thu, 08 Oct 2020 20:07:26: 4000000 INFO @ Thu, 08 Oct 2020 20:07:26: 14000000 INFO @ Thu, 08 Oct 2020 20:07:29: 9000000 INFO @ Thu, 08 Oct 2020 20:07:31: 5000000 INFO @ Thu, 08 Oct 2020 20:07:33: 15000000 INFO @ Thu, 08 Oct 2020 20:07:35: 10000000 INFO @ Thu, 08 Oct 2020 20:07:37: 6000000 INFO @ Thu, 08 Oct 2020 20:07:38: 16000000 INFO @ Thu, 08 Oct 2020 20:07:40: 11000000 INFO @ Thu, 08 Oct 2020 20:07:43: 7000000 INFO @ Thu, 08 Oct 2020 20:07:44: 17000000 INFO @ Thu, 08 Oct 2020 20:07:46: 12000000 INFO @ Thu, 08 Oct 2020 20:07:48: 8000000 INFO @ Thu, 08 Oct 2020 20:07:50: 18000000 INFO @ Thu, 08 Oct 2020 20:07:51: 13000000 INFO @ Thu, 08 Oct 2020 20:07:53: 9000000 INFO @ Thu, 08 Oct 2020 20:07:55: 19000000 INFO @ Thu, 08 Oct 2020 20:07:57: 14000000 INFO @ Thu, 08 Oct 2020 20:07:59: 10000000 INFO @ Thu, 08 Oct 2020 20:08:01: 20000000 INFO @ Thu, 08 Oct 2020 20:08:02: 15000000 INFO @ Thu, 08 Oct 2020 20:08:04: 11000000 INFO @ Thu, 08 Oct 2020 20:08:06: 21000000 INFO @ Thu, 08 Oct 2020 20:08:08: 16000000 INFO @ Thu, 08 Oct 2020 20:08:10: 12000000 INFO @ Thu, 08 Oct 2020 20:08:12: 22000000 INFO @ Thu, 08 Oct 2020 20:08:14: 17000000 INFO @ Thu, 08 Oct 2020 20:08:15: 13000000 INFO @ Thu, 08 Oct 2020 20:08:17: 23000000 INFO @ Thu, 08 Oct 2020 20:08:19: 18000000 INFO @ Thu, 08 Oct 2020 20:08:21: 14000000 INFO @ Thu, 08 Oct 2020 20:08:23: 24000000 INFO @ Thu, 08 Oct 2020 20:08:25: 19000000 INFO @ Thu, 08 Oct 2020 20:08:26: 15000000 INFO @ Thu, 08 Oct 2020 20:08:27: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:08:27: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:08:27: #1 total tags in treatment: 24657244 INFO @ Thu, 08 Oct 2020 20:08:27: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:08:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:08:27: #1 tags after filtering in treatment: 24657244 INFO @ Thu, 08 Oct 2020 20:08:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:08:27: #1 finished! INFO @ Thu, 08 Oct 2020 20:08:27: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:08:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:08:29: #2 number of paired peaks: 173 WARNING @ Thu, 08 Oct 2020 20:08:29: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Thu, 08 Oct 2020 20:08:29: start model_add_line... INFO @ Thu, 08 Oct 2020 20:08:29: start X-correlation... INFO @ Thu, 08 Oct 2020 20:08:29: end of X-cor INFO @ Thu, 08 Oct 2020 20:08:29: #2 finished! INFO @ Thu, 08 Oct 2020 20:08:29: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:08:29: #2 alternative fragment length(s) may be 1,49,550,591 bps INFO @ Thu, 08 Oct 2020 20:08:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.05_model.r WARNING @ Thu, 08 Oct 2020 20:08:29: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:08:29: #2 You may need to consider one of the other alternative d(s): 1,49,550,591 WARNING @ Thu, 08 Oct 2020 20:08:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:08:29: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:08:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:08:30: 20000000 INFO @ Thu, 08 Oct 2020 20:08:32: 16000000 INFO @ Thu, 08 Oct 2020 20:08:35: 21000000 INFO @ Thu, 08 Oct 2020 20:08:37: 17000000 INFO @ Thu, 08 Oct 2020 20:08:40: 22000000 INFO @ Thu, 08 Oct 2020 20:08:43: 18000000 INFO @ Thu, 08 Oct 2020 20:08:45: 23000000 INFO @ Thu, 08 Oct 2020 20:08:48: 19000000 INFO @ Thu, 08 Oct 2020 20:08:51: 24000000 INFO @ Thu, 08 Oct 2020 20:08:53: 20000000 INFO @ Thu, 08 Oct 2020 20:08:54: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:08:54: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:08:54: #1 total tags in treatment: 24657244 INFO @ Thu, 08 Oct 2020 20:08:54: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:08:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:08:55: #1 tags after filtering in treatment: 24657244 INFO @ Thu, 08 Oct 2020 20:08:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:08:55: #1 finished! INFO @ Thu, 08 Oct 2020 20:08:55: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:08:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:08:56: #2 number of paired peaks: 173 WARNING @ Thu, 08 Oct 2020 20:08:56: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Thu, 08 Oct 2020 20:08:56: start model_add_line... INFO @ Thu, 08 Oct 2020 20:08:56: start X-correlation... INFO @ Thu, 08 Oct 2020 20:08:56: end of X-cor INFO @ Thu, 08 Oct 2020 20:08:56: #2 finished! INFO @ Thu, 08 Oct 2020 20:08:56: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:08:56: #2 alternative fragment length(s) may be 1,49,550,591 bps INFO @ Thu, 08 Oct 2020 20:08:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.10_model.r WARNING @ Thu, 08 Oct 2020 20:08:56: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:08:56: #2 You may need to consider one of the other alternative d(s): 1,49,550,591 WARNING @ Thu, 08 Oct 2020 20:08:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:08:56: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:08:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:08:59: 21000000 INFO @ Thu, 08 Oct 2020 20:09:02: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:09:04: 22000000 INFO @ Thu, 08 Oct 2020 20:09:09: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:09:14: 24000000 INFO @ Thu, 08 Oct 2020 20:09:18: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:09:18: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:09:18: #1 total tags in treatment: 24657244 INFO @ Thu, 08 Oct 2020 20:09:18: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:09:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:09:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:09:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:09:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.05_summits.bed INFO @ Thu, 08 Oct 2020 20:09:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:09:18: #1 tags after filtering in treatment: 24657244 INFO @ Thu, 08 Oct 2020 20:09:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:09:18: #1 finished! INFO @ Thu, 08 Oct 2020 20:09:18: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:09:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:09:20: #2 number of paired peaks: 173 WARNING @ Thu, 08 Oct 2020 20:09:20: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Thu, 08 Oct 2020 20:09:20: start model_add_line... INFO @ Thu, 08 Oct 2020 20:09:20: start X-correlation... INFO @ Thu, 08 Oct 2020 20:09:20: end of X-cor INFO @ Thu, 08 Oct 2020 20:09:20: #2 finished! INFO @ Thu, 08 Oct 2020 20:09:20: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:09:20: #2 alternative fragment length(s) may be 1,49,550,591 bps INFO @ Thu, 08 Oct 2020 20:09:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.20_model.r WARNING @ Thu, 08 Oct 2020 20:09:20: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:09:20: #2 You may need to consider one of the other alternative d(s): 1,49,550,591 WARNING @ Thu, 08 Oct 2020 20:09:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:09:20: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:09:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:09:28: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:09:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:09:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:09:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.10_summits.bed INFO @ Thu, 08 Oct 2020 20:09:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:09:53: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:10:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:10:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:10:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120607/SRX9120607.20_summits.bed INFO @ Thu, 08 Oct 2020 20:10:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。