Job ID = 16434979 SRX = SRX11633393 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: 00:04:22 14335432 reads; of these: 14335432 (100.00%) were unpaired; of these: 1383265 (9.65%) aligned 0 times 11040685 (77.02%) aligned exactly 1 time 1911482 (13.33%) aligned >1 times 90.35% overall alignment rate Time searching: 00:04:22 Overall time: 00:04:22 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] 3235807 / 12952167 = 0.2498 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:34:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.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 @ Tue, 02 Aug 2022 10:34:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:34:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:34:44: 1000000 INFO @ Tue, 02 Aug 2022 10:34:50: 2000000 INFO @ Tue, 02 Aug 2022 10:34:57: 3000000 INFO @ Tue, 02 Aug 2022 10:35:03: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:35:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.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 @ Tue, 02 Aug 2022 10:35:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:35:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:35:10: 5000000 INFO @ Tue, 02 Aug 2022 10:35:15: 1000000 INFO @ Tue, 02 Aug 2022 10:35:18: 6000000 INFO @ Tue, 02 Aug 2022 10:35:22: 2000000 INFO @ Tue, 02 Aug 2022 10:35:26: 7000000 INFO @ Tue, 02 Aug 2022 10:35:30: 3000000 INFO @ Tue, 02 Aug 2022 10:35:34: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:35:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.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 @ Tue, 02 Aug 2022 10:35:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:35:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:35:38: 4000000 INFO @ Tue, 02 Aug 2022 10:35:41: 9000000 INFO @ Tue, 02 Aug 2022 10:35:46: 5000000 INFO @ Tue, 02 Aug 2022 10:35:46: 1000000 INFO @ Tue, 02 Aug 2022 10:35:47: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:35:47: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:35:47: #1 total tags in treatment: 9716360 INFO @ Tue, 02 Aug 2022 10:35:47: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:35:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:35:47: #1 tags after filtering in treatment: 9716360 INFO @ Tue, 02 Aug 2022 10:35:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:35:47: #1 finished! INFO @ Tue, 02 Aug 2022 10:35:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:35:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:35:48: #2 number of paired peaks: 279 WARNING @ Tue, 02 Aug 2022 10:35:48: Fewer paired peaks (279) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 279 pairs to build model! INFO @ Tue, 02 Aug 2022 10:35:48: start model_add_line... INFO @ Tue, 02 Aug 2022 10:35:48: start X-correlation... INFO @ Tue, 02 Aug 2022 10:35:48: end of X-cor INFO @ Tue, 02 Aug 2022 10:35:48: #2 finished! INFO @ Tue, 02 Aug 2022 10:35:48: #2 predicted fragment length is 67 bps INFO @ Tue, 02 Aug 2022 10:35:48: #2 alternative fragment length(s) may be 67 bps INFO @ Tue, 02 Aug 2022 10:35:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.05_model.r WARNING @ Tue, 02 Aug 2022 10:35:48: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:35:48: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Tue, 02 Aug 2022 10:35:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:35:48: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:35:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:35:54: 6000000 INFO @ Tue, 02 Aug 2022 10:35:56: 2000000 INFO @ Tue, 02 Aug 2022 10:36:02: 7000000 INFO @ Tue, 02 Aug 2022 10:36:04: 3000000 INFO @ Tue, 02 Aug 2022 10:36:07: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:36:10: 8000000 INFO @ Tue, 02 Aug 2022 10:36:13: 4000000 INFO @ Tue, 02 Aug 2022 10:36:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:36:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:36:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.05_summits.bed INFO @ Tue, 02 Aug 2022 10:36:17: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (524 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:36:18: 9000000 INFO @ Tue, 02 Aug 2022 10:36:22: 5000000 INFO @ Tue, 02 Aug 2022 10:36:24: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:36:24: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:36:24: #1 total tags in treatment: 9716360 INFO @ Tue, 02 Aug 2022 10:36:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:36:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:36:24: #1 tags after filtering in treatment: 9716360 INFO @ Tue, 02 Aug 2022 10:36:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:36:24: #1 finished! INFO @ Tue, 02 Aug 2022 10:36:24: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:36:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:36:24: #2 number of paired peaks: 279 WARNING @ Tue, 02 Aug 2022 10:36:24: Fewer paired peaks (279) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 279 pairs to build model! INFO @ Tue, 02 Aug 2022 10:36:24: start model_add_line... INFO @ Tue, 02 Aug 2022 10:36:24: start X-correlation... INFO @ Tue, 02 Aug 2022 10:36:24: end of X-cor INFO @ Tue, 02 Aug 2022 10:36:24: #2 finished! INFO @ Tue, 02 Aug 2022 10:36:24: #2 predicted fragment length is 67 bps INFO @ Tue, 02 Aug 2022 10:36:24: #2 alternative fragment length(s) may be 67 bps INFO @ Tue, 02 Aug 2022 10:36:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.10_model.r WARNING @ Tue, 02 Aug 2022 10:36:24: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:36:24: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Tue, 02 Aug 2022 10:36:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:36:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:36:24: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:36:31: 6000000 INFO @ Tue, 02 Aug 2022 10:36:39: 7000000 INFO @ Tue, 02 Aug 2022 10:36:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:36:47: 8000000 INFO @ Tue, 02 Aug 2022 10:36:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:36:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:36:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.10_summits.bed INFO @ Tue, 02 Aug 2022 10:36:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (326 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:36:55: 9000000 INFO @ Tue, 02 Aug 2022 10:37:01: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:37:01: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:37:01: #1 total tags in treatment: 9716360 INFO @ Tue, 02 Aug 2022 10:37:01: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:37:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:37:01: #1 tags after filtering in treatment: 9716360 INFO @ Tue, 02 Aug 2022 10:37:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:37:01: #1 finished! INFO @ Tue, 02 Aug 2022 10:37:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:37:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:37:02: #2 number of paired peaks: 279 WARNING @ Tue, 02 Aug 2022 10:37:02: Fewer paired peaks (279) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 279 pairs to build model! INFO @ Tue, 02 Aug 2022 10:37:02: start model_add_line... INFO @ Tue, 02 Aug 2022 10:37:02: start X-correlation... INFO @ Tue, 02 Aug 2022 10:37:02: end of X-cor INFO @ Tue, 02 Aug 2022 10:37:02: #2 finished! INFO @ Tue, 02 Aug 2022 10:37:02: #2 predicted fragment length is 67 bps INFO @ Tue, 02 Aug 2022 10:37:02: #2 alternative fragment length(s) may be 67 bps INFO @ Tue, 02 Aug 2022 10:37:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.20_model.r WARNING @ Tue, 02 Aug 2022 10:37:02: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:37:02: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Tue, 02 Aug 2022 10:37:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:37:02: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:37:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:37:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:37:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:37:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:37:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX11633393/SRX11633393.20_summits.bed INFO @ Tue, 02 Aug 2022 10:37:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (157 records, 4 fields): 10 millis CompletedMACS2peakCalling