Job ID = 14159439 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: 00:06:14 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: 00:06:14 Overall time: 00:06:14 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 22:00:15: # 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 @ Wed, 08 Dec 2021 22:00:15: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:00:15: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:00:21: 1000000 INFO @ Wed, 08 Dec 2021 22:00:26: 2000000 INFO @ Wed, 08 Dec 2021 22:00:32: 3000000 INFO @ Wed, 08 Dec 2021 22:00:37: 4000000 INFO @ Wed, 08 Dec 2021 22:00:42: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 22:00:45: # 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 @ Wed, 08 Dec 2021 22:00:45: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:00:45: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:00:48: 6000000 INFO @ Wed, 08 Dec 2021 22:00:50: 1000000 INFO @ Wed, 08 Dec 2021 22:00:53: 7000000 INFO @ Wed, 08 Dec 2021 22:00:56: 2000000 INFO @ Wed, 08 Dec 2021 22:00:59: 8000000 INFO @ Wed, 08 Dec 2021 22:01:01: 3000000 INFO @ Wed, 08 Dec 2021 22:01:04: 9000000 INFO @ Wed, 08 Dec 2021 22:01:07: 4000000 INFO @ Wed, 08 Dec 2021 22:01:10: 10000000 INFO @ Wed, 08 Dec 2021 22:01:12: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 22:01:15: # 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 @ Wed, 08 Dec 2021 22:01:15: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:01:15: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:01:16: 11000000 INFO @ Wed, 08 Dec 2021 22:01:18: 6000000 INFO @ Wed, 08 Dec 2021 22:01:20: 1000000 INFO @ Wed, 08 Dec 2021 22:01:21: 12000000 INFO @ Wed, 08 Dec 2021 22:01:23: 7000000 INFO @ Wed, 08 Dec 2021 22:01:24: 2000000 INFO @ Wed, 08 Dec 2021 22:01:27: 13000000 INFO @ Wed, 08 Dec 2021 22:01:29: 8000000 INFO @ Wed, 08 Dec 2021 22:01:29: 3000000 INFO @ Wed, 08 Dec 2021 22:01:32: 14000000 INFO @ Wed, 08 Dec 2021 22:01:34: 4000000 INFO @ Wed, 08 Dec 2021 22:01:34: 9000000 INFO @ Wed, 08 Dec 2021 22:01:38: 15000000 INFO @ Wed, 08 Dec 2021 22:01:39: 5000000 INFO @ Wed, 08 Dec 2021 22:01:40: 10000000 INFO @ Wed, 08 Dec 2021 22:01:43: 16000000 INFO @ Wed, 08 Dec 2021 22:01:43: 6000000 INFO @ Wed, 08 Dec 2021 22:01:46: 11000000 INFO @ Wed, 08 Dec 2021 22:01:48: 7000000 INFO @ Wed, 08 Dec 2021 22:01:49: 17000000 INFO @ Wed, 08 Dec 2021 22:01:51: 12000000 INFO @ Wed, 08 Dec 2021 22:01:53: 8000000 INFO @ Wed, 08 Dec 2021 22:01:54: 18000000 INFO @ Wed, 08 Dec 2021 22:01:57: 13000000 INFO @ Wed, 08 Dec 2021 22:01:58: 9000000 INFO @ Wed, 08 Dec 2021 22:01:59: 19000000 INFO @ Wed, 08 Dec 2021 22:02:02: 14000000 INFO @ Wed, 08 Dec 2021 22:02:02: 10000000 INFO @ Wed, 08 Dec 2021 22:02:05: 20000000 INFO @ Wed, 08 Dec 2021 22:02:07: 11000000 INFO @ Wed, 08 Dec 2021 22:02:08: 15000000 INFO @ Wed, 08 Dec 2021 22:02:10: 21000000 INFO @ Wed, 08 Dec 2021 22:02:12: 12000000 INFO @ Wed, 08 Dec 2021 22:02:13: 16000000 INFO @ Wed, 08 Dec 2021 22:02:16: 22000000 INFO @ Wed, 08 Dec 2021 22:02:17: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 22:02:17: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 22:02:17: #1 total tags in treatment: 22147091 INFO @ Wed, 08 Dec 2021 22:02:17: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:02:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:02:17: 13000000 INFO @ Wed, 08 Dec 2021 22:02:17: #1 tags after filtering in treatment: 22147091 INFO @ Wed, 08 Dec 2021 22:02:17: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:02:17: #1 finished! INFO @ Wed, 08 Dec 2021 22:02:17: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:02:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:02:18: #2 number of paired peaks: 166 WARNING @ Wed, 08 Dec 2021 22:02:18: 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 @ Wed, 08 Dec 2021 22:02:18: start model_add_line... INFO @ Wed, 08 Dec 2021 22:02:18: start X-correlation... INFO @ Wed, 08 Dec 2021 22:02:18: end of X-cor INFO @ Wed, 08 Dec 2021 22:02:18: #2 finished! INFO @ Wed, 08 Dec 2021 22:02:18: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 22:02:18: #2 alternative fragment length(s) may be 1,17,25,39,540 bps INFO @ Wed, 08 Dec 2021 22:02:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.05_model.r WARNING @ Wed, 08 Dec 2021 22:02:18: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:02:18: #2 You may need to consider one of the other alternative d(s): 1,17,25,39,540 WARNING @ Wed, 08 Dec 2021 22:02:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:02:18: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:02:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:02:19: 17000000 INFO @ Wed, 08 Dec 2021 22:02:21: 14000000 INFO @ Wed, 08 Dec 2021 22:02:24: 18000000 INFO @ Wed, 08 Dec 2021 22:02:26: 15000000 INFO @ Wed, 08 Dec 2021 22:02:29: 19000000 INFO @ Wed, 08 Dec 2021 22:02:31: 16000000 INFO @ Wed, 08 Dec 2021 22:02:35: 20000000 INFO @ Wed, 08 Dec 2021 22:02:35: 17000000 INFO @ Wed, 08 Dec 2021 22:02:40: 18000000 INFO @ Wed, 08 Dec 2021 22:02:40: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:02:45: 19000000 INFO @ Wed, 08 Dec 2021 22:02:46: 22000000 INFO @ Wed, 08 Dec 2021 22:02:46: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 22:02:46: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 22:02:46: #1 total tags in treatment: 22147091 INFO @ Wed, 08 Dec 2021 22:02:46: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:02:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:02:47: #1 tags after filtering in treatment: 22147091 INFO @ Wed, 08 Dec 2021 22:02:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:02:47: #1 finished! INFO @ Wed, 08 Dec 2021 22:02:47: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:02:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:02:48: #2 number of paired peaks: 166 WARNING @ Wed, 08 Dec 2021 22:02:48: 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 @ Wed, 08 Dec 2021 22:02:48: start model_add_line... INFO @ Wed, 08 Dec 2021 22:02:48: start X-correlation... INFO @ Wed, 08 Dec 2021 22:02:48: end of X-cor INFO @ Wed, 08 Dec 2021 22:02:48: #2 finished! INFO @ Wed, 08 Dec 2021 22:02:48: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 22:02:48: #2 alternative fragment length(s) may be 1,17,25,39,540 bps INFO @ Wed, 08 Dec 2021 22:02:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.10_model.r WARNING @ Wed, 08 Dec 2021 22:02:48: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:02:48: #2 You may need to consider one of the other alternative d(s): 1,17,25,39,540 WARNING @ Wed, 08 Dec 2021 22:02:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:02:48: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:02:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:02:49: 20000000 INFO @ Wed, 08 Dec 2021 22:02:51: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:02:54: 21000000 INFO @ Wed, 08 Dec 2021 22:02:58: 22000000 INFO @ Wed, 08 Dec 2021 22:02:59: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 22:02:59: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 22:02:59: #1 total tags in treatment: 22147091 INFO @ Wed, 08 Dec 2021 22:02:59: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:02:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:03:00: #1 tags after filtering in treatment: 22147091 INFO @ Wed, 08 Dec 2021 22:03:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:03:00: #1 finished! INFO @ Wed, 08 Dec 2021 22:03:00: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:03:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:03:01: #2 number of paired peaks: 166 WARNING @ Wed, 08 Dec 2021 22:03:01: 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 @ Wed, 08 Dec 2021 22:03:01: start model_add_line... INFO @ Wed, 08 Dec 2021 22:03:01: start X-correlation... INFO @ Wed, 08 Dec 2021 22:03:01: end of X-cor INFO @ Wed, 08 Dec 2021 22:03:01: #2 finished! INFO @ Wed, 08 Dec 2021 22:03:01: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 22:03:01: #2 alternative fragment length(s) may be 1,17,25,39,540 bps INFO @ Wed, 08 Dec 2021 22:03:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.20_model.r WARNING @ Wed, 08 Dec 2021 22:03:01: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:03:01: #2 You may need to consider one of the other alternative d(s): 1,17,25,39,540 WARNING @ Wed, 08 Dec 2021 22:03:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:03:01: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:03:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:03:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:03:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:03:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.05_summits.bed INFO @ Wed, 08 Dec 2021 22:03:07: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:03:21: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:03:33: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:03:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:03:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:03:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.10_summits.bed INFO @ Wed, 08 Dec 2021 22:03:36: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:03:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:03:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:03:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120617/SRX9120617.20_summits.bed INFO @ Wed, 08 Dec 2021 22:03:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling