Job ID = 10166112 SRX = SRX9120617 Genome = ce11 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: 00:05:48 27905994 reads; of these: 27905994 (100.00%) were unpaired; of these: 1404524 (5.03%) aligned 0 times 22147381 (79.36%) aligned exactly 1 time 4354089 (15.60%) aligned >1 times 94.97% overall alignment rate Time searching: 00:05:48 Overall time: 00:05:48 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 12 files... [bam_rmdupse_core] 4354379 / 26501470 = 0.1643 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 20:42:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.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 20:42:25: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:42:25: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:42:30: 1000000 INFO @ Thu, 08 Oct 2020 20:42:35: 2000000 INFO @ Thu, 08 Oct 2020 20:42:39: 3000000 INFO @ Thu, 08 Oct 2020 20:42:44: 4000000 INFO @ Thu, 08 Oct 2020 20:42:48: 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 20:42:53: 6000000 INFO @ Thu, 08 Oct 2020 20:42:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.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 20:42:54: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:42:54: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:42:58: 7000000 INFO @ Thu, 08 Oct 2020 20:42:59: 1000000 INFO @ Thu, 08 Oct 2020 20:43:02: 8000000 INFO @ Thu, 08 Oct 2020 20:43:04: 2000000 INFO @ Thu, 08 Oct 2020 20:43:07: 9000000 INFO @ Thu, 08 Oct 2020 20:43:09: 3000000 INFO @ Thu, 08 Oct 2020 20:43:12: 10000000 INFO @ Thu, 08 Oct 2020 20:43:14: 4000000 INFO @ Thu, 08 Oct 2020 20:43:16: 11000000 INFO @ Thu, 08 Oct 2020 20:43:18: 5000000 INFO @ Thu, 08 Oct 2020 20:43:21: 12000000 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 20:43:23: 6000000 INFO @ Thu, 08 Oct 2020 20:43:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.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 20:43:24: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:43:24: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:43:25: 13000000 INFO @ Thu, 08 Oct 2020 20:43:28: 7000000 INFO @ Thu, 08 Oct 2020 20:43:30: 1000000 INFO @ Thu, 08 Oct 2020 20:43:30: 14000000 INFO @ Thu, 08 Oct 2020 20:43:33: 8000000 INFO @ Thu, 08 Oct 2020 20:43:34: 2000000 INFO @ Thu, 08 Oct 2020 20:43:35: 15000000 INFO @ Thu, 08 Oct 2020 20:43:37: 9000000 INFO @ Thu, 08 Oct 2020 20:43:39: 3000000 INFO @ Thu, 08 Oct 2020 20:43:39: 16000000 INFO @ Thu, 08 Oct 2020 20:43:42: 10000000 INFO @ Thu, 08 Oct 2020 20:43:44: 4000000 INFO @ Thu, 08 Oct 2020 20:43:44: 17000000 INFO @ Thu, 08 Oct 2020 20:43:47: 11000000 INFO @ Thu, 08 Oct 2020 20:43:49: 5000000 INFO @ Thu, 08 Oct 2020 20:43:49: 18000000 INFO @ Thu, 08 Oct 2020 20:43:51: 12000000 INFO @ Thu, 08 Oct 2020 20:43:53: 19000000 INFO @ Thu, 08 Oct 2020 20:43:53: 6000000 INFO @ Thu, 08 Oct 2020 20:43:56: 13000000 INFO @ Thu, 08 Oct 2020 20:43:58: 20000000 INFO @ Thu, 08 Oct 2020 20:43:58: 7000000 INFO @ Thu, 08 Oct 2020 20:44:01: 14000000 INFO @ Thu, 08 Oct 2020 20:44:03: 21000000 INFO @ Thu, 08 Oct 2020 20:44:03: 8000000 INFO @ Thu, 08 Oct 2020 20:44:05: 15000000 INFO @ Thu, 08 Oct 2020 20:44:08: 9000000 INFO @ Thu, 08 Oct 2020 20:44:08: 22000000 INFO @ Thu, 08 Oct 2020 20:44:08: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:44:08: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:44:08: #1 total tags in treatment: 22147091 INFO @ Thu, 08 Oct 2020 20:44:08: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:44:08: #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 20:44:09: #1 tags after filtering in treatment: 22147091 INFO @ Thu, 08 Oct 2020 20:44:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:44:09: #1 finished! INFO @ Thu, 08 Oct 2020 20:44:09: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:44:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:44:10: 16000000 INFO @ Thu, 08 Oct 2020 20:44:10: #2 number of paired peaks: 166 WARNING @ Thu, 08 Oct 2020 20:44:10: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Thu, 08 Oct 2020 20:44:10: start model_add_line... INFO @ Thu, 08 Oct 2020 20:44:10: start X-correlation... INFO @ Thu, 08 Oct 2020 20:44:10: end of X-cor INFO @ Thu, 08 Oct 2020 20:44:10: #2 finished! INFO @ Thu, 08 Oct 2020 20:44:10: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:44:10: #2 alternative fragment length(s) may be 1,17,25,39,540 bps INFO @ Thu, 08 Oct 2020 20:44:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.05_model.r WARNING @ Thu, 08 Oct 2020 20:44:10: #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 20:44:10: #2 You may need to consider one of the other alternative d(s): 1,17,25,39,540 WARNING @ Thu, 08 Oct 2020 20:44:10: #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 20:44:10: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:44:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:44:12: 10000000 INFO @ Thu, 08 Oct 2020 20:44:14: 17000000 INFO @ Thu, 08 Oct 2020 20:44:17: 11000000 INFO @ Thu, 08 Oct 2020 20:44:19: 18000000 INFO @ Thu, 08 Oct 2020 20:44:22: 12000000 INFO @ Thu, 08 Oct 2020 20:44:24: 19000000 INFO @ Thu, 08 Oct 2020 20:44:26: 13000000 INFO @ Thu, 08 Oct 2020 20:44:29: 20000000 INFO @ Thu, 08 Oct 2020 20:44:31: 14000000 INFO @ Thu, 08 Oct 2020 20:44:33: 21000000 INFO @ Thu, 08 Oct 2020 20:44:36: 15000000 INFO @ Thu, 08 Oct 2020 20:44:38: 22000000 INFO @ Thu, 08 Oct 2020 20:44:39: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:44:39: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:44:39: #1 total tags in treatment: 22147091 INFO @ Thu, 08 Oct 2020 20:44:39: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:44:39: #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 20:44:39: #1 tags after filtering in treatment: 22147091 INFO @ Thu, 08 Oct 2020 20:44:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:44:39: #1 finished! INFO @ Thu, 08 Oct 2020 20:44:39: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:44:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:44:40: 16000000 INFO @ Thu, 08 Oct 2020 20:44:41: #2 number of paired peaks: 166 WARNING @ Thu, 08 Oct 2020 20:44:41: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Thu, 08 Oct 2020 20:44:41: start model_add_line... INFO @ Thu, 08 Oct 2020 20:44:41: start X-correlation... INFO @ Thu, 08 Oct 2020 20:44:41: end of X-cor INFO @ Thu, 08 Oct 2020 20:44:41: #2 finished! INFO @ Thu, 08 Oct 2020 20:44:41: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:44:41: #2 alternative fragment length(s) may be 1,17,25,39,540 bps INFO @ Thu, 08 Oct 2020 20:44:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.10_model.r WARNING @ Thu, 08 Oct 2020 20:44:41: #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 20:44:41: #2 You may need to consider one of the other alternative d(s): 1,17,25,39,540 WARNING @ Thu, 08 Oct 2020 20:44:41: #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 20:44:41: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:44:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:44:44: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:44:45: 17000000 INFO @ Thu, 08 Oct 2020 20:44:49: 18000000 INFO @ Thu, 08 Oct 2020 20:44:54: 19000000 INFO @ Thu, 08 Oct 2020 20:44:58: 20000000 INFO @ Thu, 08 Oct 2020 20:44:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:44:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:44:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.05_summits.bed INFO @ Thu, 08 Oct 2020 20:44:59: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:45:03: 21000000 INFO @ Thu, 08 Oct 2020 20:45:08: 22000000 INFO @ Thu, 08 Oct 2020 20:45:08: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:45:08: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:45:08: #1 total tags in treatment: 22147091 INFO @ Thu, 08 Oct 2020 20:45:08: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:45:08: #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 20:45:09: #1 tags after filtering in treatment: 22147091 INFO @ Thu, 08 Oct 2020 20:45:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:45:09: #1 finished! INFO @ Thu, 08 Oct 2020 20:45:09: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:45:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:45:10: #2 number of paired peaks: 166 WARNING @ Thu, 08 Oct 2020 20:45:10: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Thu, 08 Oct 2020 20:45:10: start model_add_line... INFO @ Thu, 08 Oct 2020 20:45:10: start X-correlation... INFO @ Thu, 08 Oct 2020 20:45:10: end of X-cor INFO @ Thu, 08 Oct 2020 20:45:10: #2 finished! INFO @ Thu, 08 Oct 2020 20:45:10: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:45:10: #2 alternative fragment length(s) may be 1,17,25,39,540 bps INFO @ Thu, 08 Oct 2020 20:45:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.20_model.r WARNING @ Thu, 08 Oct 2020 20:45:10: #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 20:45:10: #2 You may need to consider one of the other alternative d(s): 1,17,25,39,540 WARNING @ Thu, 08 Oct 2020 20:45:10: #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 20:45:10: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:45:10: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:45:14: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:45:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:45:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:45:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.10_summits.bed INFO @ Thu, 08 Oct 2020 20:45:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:45:44: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:46:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:46:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:46:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.20_summits.bed INFO @ Thu, 08 Oct 2020 20:46:00: 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。