Job ID = 14159413 SRX = SRX9120613 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: 00:08:28 37768674 reads; of these: 37768674 (100.00%) were unpaired; of these: 12273079 (32.50%) aligned 0 times 21159682 (56.02%) aligned exactly 1 time 4335913 (11.48%) aligned >1 times 67.50% overall alignment rate Time searching: 00:08:28 Overall time: 00:08:28 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] 4316710 / 25495595 = 0.1693 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 21:49:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.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 21:49:17: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:49:17: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:49:27: 1000000 INFO @ Wed, 08 Dec 2021 21:49:37: 2000000 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 21:49:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.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 21:49:46: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:49:46: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:49:47: 3000000 INFO @ Wed, 08 Dec 2021 21:49:54: 1000000 INFO @ Wed, 08 Dec 2021 21:49:57: 4000000 INFO @ Wed, 08 Dec 2021 21:50:02: 2000000 INFO @ Wed, 08 Dec 2021 21:50:07: 5000000 INFO @ Wed, 08 Dec 2021 21:50:09: 3000000 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 21:50:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.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 21:50:16: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:50:16: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:50:17: 4000000 INFO @ Wed, 08 Dec 2021 21:50:17: 6000000 INFO @ Wed, 08 Dec 2021 21:50:24: 5000000 INFO @ Wed, 08 Dec 2021 21:50:27: 1000000 INFO @ Wed, 08 Dec 2021 21:50:28: 7000000 INFO @ Wed, 08 Dec 2021 21:50:32: 6000000 INFO @ Wed, 08 Dec 2021 21:50:38: 2000000 INFO @ Wed, 08 Dec 2021 21:50:39: 8000000 INFO @ Wed, 08 Dec 2021 21:50:39: 7000000 INFO @ Wed, 08 Dec 2021 21:50:47: 8000000 INFO @ Wed, 08 Dec 2021 21:50:49: 3000000 INFO @ Wed, 08 Dec 2021 21:50:50: 9000000 INFO @ Wed, 08 Dec 2021 21:50:54: 9000000 INFO @ Wed, 08 Dec 2021 21:51:01: 4000000 INFO @ Wed, 08 Dec 2021 21:51:01: 10000000 INFO @ Wed, 08 Dec 2021 21:51:02: 10000000 INFO @ Wed, 08 Dec 2021 21:51:09: 11000000 INFO @ Wed, 08 Dec 2021 21:51:11: 5000000 INFO @ Wed, 08 Dec 2021 21:51:13: 11000000 INFO @ Wed, 08 Dec 2021 21:51:17: 12000000 INFO @ Wed, 08 Dec 2021 21:51:22: 6000000 INFO @ Wed, 08 Dec 2021 21:51:24: 12000000 INFO @ Wed, 08 Dec 2021 21:51:24: 13000000 INFO @ Wed, 08 Dec 2021 21:51:32: 14000000 INFO @ Wed, 08 Dec 2021 21:51:33: 7000000 INFO @ Wed, 08 Dec 2021 21:51:35: 13000000 INFO @ Wed, 08 Dec 2021 21:51:39: 15000000 INFO @ Wed, 08 Dec 2021 21:51:44: 8000000 INFO @ Wed, 08 Dec 2021 21:51:46: 14000000 INFO @ Wed, 08 Dec 2021 21:51:46: 16000000 INFO @ Wed, 08 Dec 2021 21:51:54: 17000000 INFO @ Wed, 08 Dec 2021 21:51:55: 9000000 INFO @ Wed, 08 Dec 2021 21:51:57: 15000000 INFO @ Wed, 08 Dec 2021 21:52:01: 18000000 INFO @ Wed, 08 Dec 2021 21:52:06: 10000000 INFO @ Wed, 08 Dec 2021 21:52:08: 19000000 INFO @ Wed, 08 Dec 2021 21:52:09: 16000000 INFO @ Wed, 08 Dec 2021 21:52:16: 20000000 INFO @ Wed, 08 Dec 2021 21:52:17: 11000000 INFO @ Wed, 08 Dec 2021 21:52:20: 17000000 INFO @ Wed, 08 Dec 2021 21:52:23: 21000000 INFO @ Wed, 08 Dec 2021 21:52:25: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 21:52:25: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 21:52:25: #1 total tags in treatment: 21178885 INFO @ Wed, 08 Dec 2021 21:52:25: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:52:25: #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 21:52:25: #1 tags after filtering in treatment: 21178885 INFO @ Wed, 08 Dec 2021 21:52:25: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:52:25: #1 finished! INFO @ Wed, 08 Dec 2021 21:52:25: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:52:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:52:27: #2 number of paired peaks: 195 WARNING @ Wed, 08 Dec 2021 21:52:27: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Wed, 08 Dec 2021 21:52:27: start model_add_line... INFO @ Wed, 08 Dec 2021 21:52:27: start X-correlation... INFO @ Wed, 08 Dec 2021 21:52:27: end of X-cor INFO @ Wed, 08 Dec 2021 21:52:27: #2 finished! INFO @ Wed, 08 Dec 2021 21:52:27: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 21:52:27: #2 alternative fragment length(s) may be 1,26,595 bps INFO @ Wed, 08 Dec 2021 21:52:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.10_model.r WARNING @ Wed, 08 Dec 2021 21:52:27: #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 21:52:27: #2 You may need to consider one of the other alternative d(s): 1,26,595 WARNING @ Wed, 08 Dec 2021 21:52:27: #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 21:52:27: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:52:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:52:29: 12000000 INFO @ Wed, 08 Dec 2021 21:52:31: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:52:39: 13000000 INFO @ Wed, 08 Dec 2021 21:52:42: 19000000 INFO @ Wed, 08 Dec 2021 21:52:50: 14000000 INFO @ Wed, 08 Dec 2021 21:52:53: 20000000 INFO @ Wed, 08 Dec 2021 21:53:01: 15000000 INFO @ Wed, 08 Dec 2021 21:53:03: 21000000 INFO @ Wed, 08 Dec 2021 21:53:05: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 21:53:05: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 21:53:05: #1 total tags in treatment: 21178885 INFO @ Wed, 08 Dec 2021 21:53:05: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:53:05: #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 21:53:05: #1 tags after filtering in treatment: 21178885 INFO @ Wed, 08 Dec 2021 21:53:05: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:53:05: #1 finished! INFO @ Wed, 08 Dec 2021 21:53:05: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:53:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:53:07: #2 number of paired peaks: 195 WARNING @ Wed, 08 Dec 2021 21:53:07: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Wed, 08 Dec 2021 21:53:07: start model_add_line... INFO @ Wed, 08 Dec 2021 21:53:07: start X-correlation... INFO @ Wed, 08 Dec 2021 21:53:07: end of X-cor INFO @ Wed, 08 Dec 2021 21:53:07: #2 finished! INFO @ Wed, 08 Dec 2021 21:53:07: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 21:53:07: #2 alternative fragment length(s) may be 1,26,595 bps INFO @ Wed, 08 Dec 2021 21:53:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.05_model.r WARNING @ Wed, 08 Dec 2021 21:53:07: #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 21:53:07: #2 You may need to consider one of the other alternative d(s): 1,26,595 WARNING @ Wed, 08 Dec 2021 21:53:07: #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 21:53:07: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:53:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:53:11: 16000000 INFO @ Wed, 08 Dec 2021 21:53:12: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:53:20: 17000000 INFO @ Wed, 08 Dec 2021 21:53:30: 18000000 INFO @ Wed, 08 Dec 2021 21:53:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:53:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:53:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.10_summits.bed INFO @ Wed, 08 Dec 2021 21:53:34: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:53:39: 19000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:53:48: 20000000 INFO @ Wed, 08 Dec 2021 21:53:53: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:53:58: 21000000 INFO @ Wed, 08 Dec 2021 21:54:00: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 21:54:00: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 21:54:00: #1 total tags in treatment: 21178885 INFO @ Wed, 08 Dec 2021 21:54:00: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:54:00: #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 21:54:00: #1 tags after filtering in treatment: 21178885 INFO @ Wed, 08 Dec 2021 21:54:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:54:00: #1 finished! INFO @ Wed, 08 Dec 2021 21:54:00: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:54:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:54:02: #2 number of paired peaks: 195 WARNING @ Wed, 08 Dec 2021 21:54:02: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Wed, 08 Dec 2021 21:54:02: start model_add_line... INFO @ Wed, 08 Dec 2021 21:54:02: start X-correlation... INFO @ Wed, 08 Dec 2021 21:54:02: end of X-cor INFO @ Wed, 08 Dec 2021 21:54:02: #2 finished! INFO @ Wed, 08 Dec 2021 21:54:02: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 21:54:02: #2 alternative fragment length(s) may be 1,26,595 bps INFO @ Wed, 08 Dec 2021 21:54:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.20_model.r WARNING @ Wed, 08 Dec 2021 21:54:02: #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 21:54:02: #2 You may need to consider one of the other alternative d(s): 1,26,595 WARNING @ Wed, 08 Dec 2021 21:54:02: #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 21:54:02: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:54:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:54:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:54:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:54:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.05_summits.bed INFO @ Wed, 08 Dec 2021 21:54:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:54:47: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:55:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:55:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:55:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.20_summits.bed INFO @ Wed, 08 Dec 2021 21:55:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling