Job ID = 14159937 SRX = SRX3180774 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: 00:02:22 11006715 reads; of these: 11006715 (100.00%) were unpaired; of these: 581385 (5.28%) aligned 0 times 8285870 (75.28%) aligned exactly 1 time 2139460 (19.44%) aligned >1 times 94.72% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 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 8 files... [bam_rmdupse_core] 3856854 / 10425330 = 0.3700 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 @ Thu, 09 Dec 2021 00:45:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.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, 09 Dec 2021 00:45:06: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:45:06: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:45:12: 1000000 INFO @ Thu, 09 Dec 2021 00:45:17: 2000000 INFO @ Thu, 09 Dec 2021 00:45:23: 3000000 INFO @ Thu, 09 Dec 2021 00:45:28: 4000000 INFO @ Thu, 09 Dec 2021 00:45:34: 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 @ Thu, 09 Dec 2021 00:45:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.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, 09 Dec 2021 00:45:36: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:45:36: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:45:40: 6000000 INFO @ Thu, 09 Dec 2021 00:45:43: 1000000 INFO @ Thu, 09 Dec 2021 00:45:43: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 00:45:43: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 00:45:43: #1 total tags in treatment: 6568476 INFO @ Thu, 09 Dec 2021 00:45:43: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:45:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:45:43: #1 tags after filtering in treatment: 6568476 INFO @ Thu, 09 Dec 2021 00:45:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:45:43: #1 finished! INFO @ Thu, 09 Dec 2021 00:45:43: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:45:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:45:44: #2 number of paired peaks: 541 WARNING @ Thu, 09 Dec 2021 00:45:44: Fewer paired peaks (541) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 541 pairs to build model! INFO @ Thu, 09 Dec 2021 00:45:44: start model_add_line... INFO @ Thu, 09 Dec 2021 00:45:44: start X-correlation... INFO @ Thu, 09 Dec 2021 00:45:44: end of X-cor INFO @ Thu, 09 Dec 2021 00:45:44: #2 finished! INFO @ Thu, 09 Dec 2021 00:45:44: #2 predicted fragment length is 48 bps INFO @ Thu, 09 Dec 2021 00:45:44: #2 alternative fragment length(s) may be 3,48 bps INFO @ Thu, 09 Dec 2021 00:45:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.05_model.r WARNING @ Thu, 09 Dec 2021 00:45:44: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:45:44: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Thu, 09 Dec 2021 00:45:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 00:45:44: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:45:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:45:49: 2000000 INFO @ Thu, 09 Dec 2021 00:45:54: 3000000 INFO @ Thu, 09 Dec 2021 00:45:58: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:46:00: 4000000 INFO @ Thu, 09 Dec 2021 00:46:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:46:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:46:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.05_summits.bed INFO @ Thu, 09 Dec 2021 00:46:04: Done! 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 pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (689 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:46:05: 5000000 INFO @ Thu, 09 Dec 2021 00:46:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.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, 09 Dec 2021 00:46:07: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:46:07: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:46:11: 6000000 INFO @ Thu, 09 Dec 2021 00:46:14: 1000000 INFO @ Thu, 09 Dec 2021 00:46:15: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 00:46:15: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 00:46:15: #1 total tags in treatment: 6568476 INFO @ Thu, 09 Dec 2021 00:46:15: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:46:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:46:15: #1 tags after filtering in treatment: 6568476 INFO @ Thu, 09 Dec 2021 00:46:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:46:15: #1 finished! INFO @ Thu, 09 Dec 2021 00:46:15: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:46:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:46:16: #2 number of paired peaks: 541 WARNING @ Thu, 09 Dec 2021 00:46:16: Fewer paired peaks (541) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 541 pairs to build model! INFO @ Thu, 09 Dec 2021 00:46:16: start model_add_line... INFO @ Thu, 09 Dec 2021 00:46:16: start X-correlation... INFO @ Thu, 09 Dec 2021 00:46:16: end of X-cor INFO @ Thu, 09 Dec 2021 00:46:16: #2 finished! INFO @ Thu, 09 Dec 2021 00:46:16: #2 predicted fragment length is 48 bps INFO @ Thu, 09 Dec 2021 00:46:16: #2 alternative fragment length(s) may be 3,48 bps INFO @ Thu, 09 Dec 2021 00:46:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.10_model.r WARNING @ Thu, 09 Dec 2021 00:46:16: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:46:16: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Thu, 09 Dec 2021 00:46:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 00:46:16: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:46:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:46:21: 2000000 INFO @ Thu, 09 Dec 2021 00:46:28: 3000000 INFO @ Thu, 09 Dec 2021 00:46:29: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:46:35: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:46:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:46:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:46:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.10_summits.bed INFO @ Thu, 09 Dec 2021 00:46:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (465 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:46:42: 5000000 INFO @ Thu, 09 Dec 2021 00:46:48: 6000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:46:52: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 00:46:52: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 00:46:52: #1 total tags in treatment: 6568476 INFO @ Thu, 09 Dec 2021 00:46:52: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:46:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:46:52: #1 tags after filtering in treatment: 6568476 INFO @ Thu, 09 Dec 2021 00:46:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:46:52: #1 finished! INFO @ Thu, 09 Dec 2021 00:46:52: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:46:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:46:53: #2 number of paired peaks: 541 WARNING @ Thu, 09 Dec 2021 00:46:53: Fewer paired peaks (541) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 541 pairs to build model! INFO @ Thu, 09 Dec 2021 00:46:53: start model_add_line... INFO @ Thu, 09 Dec 2021 00:46:53: start X-correlation... INFO @ Thu, 09 Dec 2021 00:46:53: end of X-cor INFO @ Thu, 09 Dec 2021 00:46:53: #2 finished! INFO @ Thu, 09 Dec 2021 00:46:53: #2 predicted fragment length is 48 bps INFO @ Thu, 09 Dec 2021 00:46:53: #2 alternative fragment length(s) may be 3,48 bps INFO @ Thu, 09 Dec 2021 00:46:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.20_model.r WARNING @ Thu, 09 Dec 2021 00:46:53: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:46:53: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Thu, 09 Dec 2021 00:46:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 00:46:53: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:46:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:47:07: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:47:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:47:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:47:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180774/SRX3180774.20_summits.bed INFO @ Thu, 09 Dec 2021 00:47:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (194 records, 4 fields): 2 millis CompletedMACS2peakCalling