Job ID = 14160772 SRX = SRX11322241 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: 00:05:36 8439153 reads; of these: 8439153 (100.00%) were unpaired; of these: 2382506 (28.23%) aligned 0 times 5193528 (61.54%) aligned exactly 1 time 863119 (10.23%) aligned >1 times 71.77% overall alignment rate Time searching: 00:05:36 Overall time: 00:05:36 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] 918802 / 6056647 = 0.1517 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 04:17:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.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 04:17:02: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:17:02: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:17:12: 1000000 INFO @ Thu, 09 Dec 2021 04:17:23: 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 @ Thu, 09 Dec 2021 04:17:32: 3000000 INFO @ Thu, 09 Dec 2021 04:17:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.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 04:17:33: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:17:33: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:17:43: 4000000 INFO @ Thu, 09 Dec 2021 04:17:43: 1000000 INFO @ Thu, 09 Dec 2021 04:17:54: 2000000 INFO @ Thu, 09 Dec 2021 04:17:55: 5000000 INFO @ Thu, 09 Dec 2021 04:17:56: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 04:17:56: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 04:17:56: #1 total tags in treatment: 5137845 INFO @ Thu, 09 Dec 2021 04:17:56: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:17:56: #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 04:17:56: #1 tags after filtering in treatment: 5137845 INFO @ Thu, 09 Dec 2021 04:17:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:17:56: #1 finished! INFO @ Thu, 09 Dec 2021 04:17:56: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:17:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:17:57: #2 number of paired peaks: 389 WARNING @ Thu, 09 Dec 2021 04:17:57: Fewer paired peaks (389) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 389 pairs to build model! INFO @ Thu, 09 Dec 2021 04:17:57: start model_add_line... INFO @ Thu, 09 Dec 2021 04:17:57: start X-correlation... INFO @ Thu, 09 Dec 2021 04:17:57: end of X-cor INFO @ Thu, 09 Dec 2021 04:17:57: #2 finished! INFO @ Thu, 09 Dec 2021 04:17:57: #2 predicted fragment length is 147 bps INFO @ Thu, 09 Dec 2021 04:17:57: #2 alternative fragment length(s) may be 147,547,563,567 bps INFO @ Thu, 09 Dec 2021 04:17:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.05_model.r WARNING @ Thu, 09 Dec 2021 04:17:57: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:17:57: #2 You may need to consider one of the other alternative d(s): 147,547,563,567 WARNING @ Thu, 09 Dec 2021 04:17:57: #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 04:17:57: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:17:57: #3 Pre-compute pvalue-qvalue table... 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 @ Thu, 09 Dec 2021 04:18:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.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 04:18:02: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:18:02: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:18:03: 3000000 INFO @ Thu, 09 Dec 2021 04:18:08: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:18:12: 4000000 INFO @ Thu, 09 Dec 2021 04:18:12: 1000000 INFO @ Thu, 09 Dec 2021 04:18:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:18:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:18:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.05_summits.bed INFO @ Thu, 09 Dec 2021 04:18:14: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (378 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:18:21: 5000000 INFO @ Thu, 09 Dec 2021 04:18:22: 2000000 INFO @ Thu, 09 Dec 2021 04:18:23: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 04:18:23: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 04:18:23: #1 total tags in treatment: 5137845 INFO @ Thu, 09 Dec 2021 04:18:23: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:18:23: #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 04:18:23: #1 tags after filtering in treatment: 5137845 INFO @ Thu, 09 Dec 2021 04:18:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:18:23: #1 finished! INFO @ Thu, 09 Dec 2021 04:18:23: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:18:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:18:23: #2 number of paired peaks: 389 WARNING @ Thu, 09 Dec 2021 04:18:23: Fewer paired peaks (389) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 389 pairs to build model! INFO @ Thu, 09 Dec 2021 04:18:23: start model_add_line... INFO @ Thu, 09 Dec 2021 04:18:23: start X-correlation... INFO @ Thu, 09 Dec 2021 04:18:23: end of X-cor INFO @ Thu, 09 Dec 2021 04:18:23: #2 finished! INFO @ Thu, 09 Dec 2021 04:18:23: #2 predicted fragment length is 147 bps INFO @ Thu, 09 Dec 2021 04:18:23: #2 alternative fragment length(s) may be 147,547,563,567 bps INFO @ Thu, 09 Dec 2021 04:18:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.10_model.r WARNING @ Thu, 09 Dec 2021 04:18:23: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:18:23: #2 You may need to consider one of the other alternative d(s): 147,547,563,567 WARNING @ Thu, 09 Dec 2021 04:18:23: #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 04:18:23: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:18:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:18:30: 3000000 INFO @ Thu, 09 Dec 2021 04:18:35: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:18:39: 4000000 INFO @ Thu, 09 Dec 2021 04:18:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:18:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:18:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.10_summits.bed INFO @ Thu, 09 Dec 2021 04:18:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (275 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:18:47: 5000000 INFO @ Thu, 09 Dec 2021 04:18:48: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 04:18:48: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 04:18:48: #1 total tags in treatment: 5137845 INFO @ Thu, 09 Dec 2021 04:18:48: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:18:48: #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 04:18:48: #1 tags after filtering in treatment: 5137845 INFO @ Thu, 09 Dec 2021 04:18:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:18:48: #1 finished! INFO @ Thu, 09 Dec 2021 04:18:48: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:18:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:18:49: #2 number of paired peaks: 389 WARNING @ Thu, 09 Dec 2021 04:18:49: Fewer paired peaks (389) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 389 pairs to build model! INFO @ Thu, 09 Dec 2021 04:18:49: start model_add_line... INFO @ Thu, 09 Dec 2021 04:18:49: start X-correlation... INFO @ Thu, 09 Dec 2021 04:18:49: end of X-cor INFO @ Thu, 09 Dec 2021 04:18:49: #2 finished! INFO @ Thu, 09 Dec 2021 04:18:49: #2 predicted fragment length is 147 bps INFO @ Thu, 09 Dec 2021 04:18:49: #2 alternative fragment length(s) may be 147,547,563,567 bps INFO @ Thu, 09 Dec 2021 04:18:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.20_model.r WARNING @ Thu, 09 Dec 2021 04:18:49: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:18:49: #2 You may need to consider one of the other alternative d(s): 147,547,563,567 WARNING @ Thu, 09 Dec 2021 04:18:49: #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 04:18:49: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:18:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:19:00: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:19:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:19:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:19:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX11322241/SRX11322241.20_summits.bed INFO @ Thu, 09 Dec 2021 04:19:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (184 records, 4 fields): 1 millis CompletedMACS2peakCalling