Job ID = 12265587 SRX = SRX4082403 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: 00:37:20 334907090 reads; of these: 334907090 (100.00%) were unpaired; of these: 304088296 (90.80%) aligned 0 times 26887473 (8.03%) aligned exactly 1 time 3931321 (1.17%) aligned >1 times 9.20% overall alignment rate Time searching: 00:37:20 Overall time: 00:37:20 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] 17231383 / 30818794 = 0.5591 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 08:25:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.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 @ Sat, 03 Apr 2021 08:25:15: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:25:15: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:25:21: 1000000 INFO @ Sat, 03 Apr 2021 08:25:27: 2000000 INFO @ Sat, 03 Apr 2021 08:25:33: 3000000 INFO @ Sat, 03 Apr 2021 08:25:38: 4000000 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 08:25:44: 5000000 INFO @ Sat, 03 Apr 2021 08:25:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.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 @ Sat, 03 Apr 2021 08:25:45: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:25:45: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:25:50: 6000000 INFO @ Sat, 03 Apr 2021 08:25:51: 1000000 INFO @ Sat, 03 Apr 2021 08:25:56: 7000000 INFO @ Sat, 03 Apr 2021 08:25:57: 2000000 INFO @ Sat, 03 Apr 2021 08:26:02: 8000000 INFO @ Sat, 03 Apr 2021 08:26:03: 3000000 INFO @ Sat, 03 Apr 2021 08:26:08: 9000000 INFO @ Sat, 03 Apr 2021 08:26:09: 4000000 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 INFO @ Sat, 03 Apr 2021 08:26:14: 10000000 INFO @ Sat, 03 Apr 2021 08:26:15: 5000000 INFO @ Sat, 03 Apr 2021 08:26:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.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 @ Sat, 03 Apr 2021 08:26:15: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:26:15: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:26:20: 11000000 INFO @ Sat, 03 Apr 2021 08:26:21: 6000000 INFO @ Sat, 03 Apr 2021 08:26:22: 1000000 INFO @ Sat, 03 Apr 2021 08:26:26: 12000000 INFO @ Sat, 03 Apr 2021 08:26:27: 7000000 INFO @ Sat, 03 Apr 2021 08:26:28: 2000000 INFO @ Sat, 03 Apr 2021 08:26:31: 13000000 INFO @ Sat, 03 Apr 2021 08:26:33: 8000000 INFO @ Sat, 03 Apr 2021 08:26:34: 3000000 INFO @ Sat, 03 Apr 2021 08:26:35: #1 tag size is determined as 49 bps INFO @ Sat, 03 Apr 2021 08:26:35: #1 tag size = 49 INFO @ Sat, 03 Apr 2021 08:26:35: #1 total tags in treatment: 13587411 INFO @ Sat, 03 Apr 2021 08:26:35: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:26:35: #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 08:26:35: #1 tags after filtering in treatment: 13587411 INFO @ Sat, 03 Apr 2021 08:26:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:26:35: #1 finished! INFO @ Sat, 03 Apr 2021 08:26:35: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:26:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:26:36: #2 number of paired peaks: 805 WARNING @ Sat, 03 Apr 2021 08:26:36: Fewer paired peaks (805) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 805 pairs to build model! INFO @ Sat, 03 Apr 2021 08:26:36: start model_add_line... INFO @ Sat, 03 Apr 2021 08:26:36: start X-correlation... INFO @ Sat, 03 Apr 2021 08:26:36: end of X-cor INFO @ Sat, 03 Apr 2021 08:26:36: #2 finished! INFO @ Sat, 03 Apr 2021 08:26:36: #2 predicted fragment length is 71 bps INFO @ Sat, 03 Apr 2021 08:26:36: #2 alternative fragment length(s) may be 71 bps INFO @ Sat, 03 Apr 2021 08:26:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.05_model.r WARNING @ Sat, 03 Apr 2021 08:26:36: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:26:36: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Sat, 03 Apr 2021 08:26:36: #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 08:26:36: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:26:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:26:39: 9000000 INFO @ Sat, 03 Apr 2021 08:26:40: 4000000 INFO @ Sat, 03 Apr 2021 08:26:45: 10000000 INFO @ Sat, 03 Apr 2021 08:26:46: 5000000 INFO @ Sat, 03 Apr 2021 08:26:51: 11000000 INFO @ Sat, 03 Apr 2021 08:26:52: 6000000 INFO @ Sat, 03 Apr 2021 08:26:57: 12000000 INFO @ Sat, 03 Apr 2021 08:26:58: 7000000 INFO @ Sat, 03 Apr 2021 08:27:02: 13000000 INFO @ Sat, 03 Apr 2021 08:27:04: 8000000 INFO @ Sat, 03 Apr 2021 08:27:06: #1 tag size is determined as 49 bps INFO @ Sat, 03 Apr 2021 08:27:06: #1 tag size = 49 INFO @ Sat, 03 Apr 2021 08:27:06: #1 total tags in treatment: 13587411 INFO @ Sat, 03 Apr 2021 08:27:06: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:27:06: #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 08:27:06: #1 tags after filtering in treatment: 13587411 INFO @ Sat, 03 Apr 2021 08:27:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:27:06: #1 finished! INFO @ Sat, 03 Apr 2021 08:27:06: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:27:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:27:07: #2 number of paired peaks: 805 WARNING @ Sat, 03 Apr 2021 08:27:07: Fewer paired peaks (805) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 805 pairs to build model! INFO @ Sat, 03 Apr 2021 08:27:07: start model_add_line... INFO @ Sat, 03 Apr 2021 08:27:07: start X-correlation... INFO @ Sat, 03 Apr 2021 08:27:07: end of X-cor INFO @ Sat, 03 Apr 2021 08:27:07: #2 finished! INFO @ Sat, 03 Apr 2021 08:27:07: #2 predicted fragment length is 71 bps INFO @ Sat, 03 Apr 2021 08:27:07: #2 alternative fragment length(s) may be 71 bps INFO @ Sat, 03 Apr 2021 08:27:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.10_model.r WARNING @ Sat, 03 Apr 2021 08:27:07: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:27:07: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Sat, 03 Apr 2021 08:27:07: #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 08:27:07: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:27:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:27:09: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:27:10: 9000000 INFO @ Sat, 03 Apr 2021 08:27:15: 10000000 INFO @ Sat, 03 Apr 2021 08:27:21: 11000000 INFO @ Sat, 03 Apr 2021 08:27:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:27:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:27:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.05_summits.bed INFO @ Sat, 03 Apr 2021 08:27:27: Done! INFO @ Sat, 03 Apr 2021 08:27:27: 12000000 pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (15519 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:27:33: 13000000 INFO @ Sat, 03 Apr 2021 08:27:36: #1 tag size is determined as 49 bps INFO @ Sat, 03 Apr 2021 08:27:36: #1 tag size = 49 INFO @ Sat, 03 Apr 2021 08:27:36: #1 total tags in treatment: 13587411 INFO @ Sat, 03 Apr 2021 08:27:36: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:27:36: #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 08:27:36: #1 tags after filtering in treatment: 13587411 INFO @ Sat, 03 Apr 2021 08:27:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:27:36: #1 finished! INFO @ Sat, 03 Apr 2021 08:27:36: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:27:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:27:37: #2 number of paired peaks: 805 WARNING @ Sat, 03 Apr 2021 08:27:37: Fewer paired peaks (805) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 805 pairs to build model! INFO @ Sat, 03 Apr 2021 08:27:37: start model_add_line... INFO @ Sat, 03 Apr 2021 08:27:38: start X-correlation... INFO @ Sat, 03 Apr 2021 08:27:38: end of X-cor INFO @ Sat, 03 Apr 2021 08:27:38: #2 finished! INFO @ Sat, 03 Apr 2021 08:27:38: #2 predicted fragment length is 71 bps INFO @ Sat, 03 Apr 2021 08:27:38: #2 alternative fragment length(s) may be 71 bps INFO @ Sat, 03 Apr 2021 08:27:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.20_model.r WARNING @ Sat, 03 Apr 2021 08:27:38: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:27:38: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Sat, 03 Apr 2021 08:27:38: #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 08:27:38: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:27:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:27:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:27:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:27:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:27:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.10_summits.bed INFO @ Sat, 03 Apr 2021 08:27:57: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (9863 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:28:10: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:28:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:28:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:28:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082403/SRX4082403.20_summits.bed INFO @ Sat, 03 Apr 2021 08:28:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4400 records, 4 fields): 7 millis CompletedMACS2peakCalling