Job ID = 14160845 SRX = SRX11322244 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:10 10584893 reads; of these: 10584893 (100.00%) were unpaired; of these: 3170670 (29.95%) aligned 0 times 5935662 (56.08%) aligned exactly 1 time 1478561 (13.97%) aligned >1 times 70.05% overall alignment rate Time searching: 00:07:11 Overall time: 00:07:11 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] 1520522 / 7414223 = 0.2051 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 04:41:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.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 04:41:40: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:41:40: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:41:49: 1000000 INFO @ Thu, 09 Dec 2021 04:41:57: 2000000 INFO @ Thu, 09 Dec 2021 04:42:06: 3000000 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 04:42:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.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 04:42:10: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:42:10: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:42:15: 4000000 INFO @ Thu, 09 Dec 2021 04:42:23: 1000000 INFO @ Thu, 09 Dec 2021 04:42:26: 5000000 INFO @ Thu, 09 Dec 2021 04:42:35: 2000000 INFO @ Thu, 09 Dec 2021 04:42:36: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 04:42:36: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 04:42:36: #1 total tags in treatment: 5893701 INFO @ Thu, 09 Dec 2021 04:42:36: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:42:36: #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 04:42:36: #1 tags after filtering in treatment: 5893701 INFO @ Thu, 09 Dec 2021 04:42:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:42:36: #1 finished! INFO @ Thu, 09 Dec 2021 04:42:36: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:42:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:42:36: #2 number of paired peaks: 514 WARNING @ Thu, 09 Dec 2021 04:42:36: Fewer paired peaks (514) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 514 pairs to build model! INFO @ Thu, 09 Dec 2021 04:42:36: start model_add_line... INFO @ Thu, 09 Dec 2021 04:42:36: start X-correlation... INFO @ Thu, 09 Dec 2021 04:42:36: end of X-cor INFO @ Thu, 09 Dec 2021 04:42:36: #2 finished! INFO @ Thu, 09 Dec 2021 04:42:36: #2 predicted fragment length is 145 bps INFO @ Thu, 09 Dec 2021 04:42:36: #2 alternative fragment length(s) may be 145 bps INFO @ Thu, 09 Dec 2021 04:42:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.05_model.r WARNING @ Thu, 09 Dec 2021 04:42:36: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:42:36: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Thu, 09 Dec 2021 04:42:36: #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 04:42:36: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:42:36: #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 04:42:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.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 04:42:40: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:42:40: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:42:47: 3000000 INFO @ Thu, 09 Dec 2021 04:42:49: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:42:51: 1000000 INFO @ Thu, 09 Dec 2021 04:42:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:42:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:42:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.05_summits.bed INFO @ Thu, 09 Dec 2021 04:42:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (570 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:42:59: 4000000 INFO @ Thu, 09 Dec 2021 04:43:03: 2000000 INFO @ Thu, 09 Dec 2021 04:43:11: 5000000 INFO @ Thu, 09 Dec 2021 04:43:14: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:43:22: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 04:43:22: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 04:43:22: #1 total tags in treatment: 5893701 INFO @ Thu, 09 Dec 2021 04:43:22: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:43:22: #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 04:43:22: #1 tags after filtering in treatment: 5893701 INFO @ Thu, 09 Dec 2021 04:43:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:43:22: #1 finished! INFO @ Thu, 09 Dec 2021 04:43:22: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:43:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:43:23: #2 number of paired peaks: 514 WARNING @ Thu, 09 Dec 2021 04:43:23: Fewer paired peaks (514) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 514 pairs to build model! INFO @ Thu, 09 Dec 2021 04:43:23: start model_add_line... INFO @ Thu, 09 Dec 2021 04:43:23: start X-correlation... INFO @ Thu, 09 Dec 2021 04:43:23: end of X-cor INFO @ Thu, 09 Dec 2021 04:43:23: #2 finished! INFO @ Thu, 09 Dec 2021 04:43:23: #2 predicted fragment length is 145 bps INFO @ Thu, 09 Dec 2021 04:43:23: #2 alternative fragment length(s) may be 145 bps INFO @ Thu, 09 Dec 2021 04:43:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.10_model.r WARNING @ Thu, 09 Dec 2021 04:43:23: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:43:23: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Thu, 09 Dec 2021 04:43:23: #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 04:43:23: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:43:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:43:24: 4000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:43:33: 5000000 INFO @ Thu, 09 Dec 2021 04:43:35: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:43:41: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 04:43:41: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 04:43:41: #1 total tags in treatment: 5893701 INFO @ Thu, 09 Dec 2021 04:43:41: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:43:41: #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 04:43:41: #1 tags after filtering in treatment: 5893701 INFO @ Thu, 09 Dec 2021 04:43:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:43:41: #1 finished! INFO @ Thu, 09 Dec 2021 04:43:41: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:43:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:43:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:43:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:43:41: #2 number of paired peaks: 514 WARNING @ Thu, 09 Dec 2021 04:43:41: Fewer paired peaks (514) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 514 pairs to build model! INFO @ Thu, 09 Dec 2021 04:43:41: start model_add_line... INFO @ Thu, 09 Dec 2021 04:43:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.10_summits.bed INFO @ Thu, 09 Dec 2021 04:43:41: Done! INFO @ Thu, 09 Dec 2021 04:43:41: start X-correlation... INFO @ Thu, 09 Dec 2021 04:43:41: end of X-cor INFO @ Thu, 09 Dec 2021 04:43:41: #2 finished! INFO @ Thu, 09 Dec 2021 04:43:41: #2 predicted fragment length is 145 bps INFO @ Thu, 09 Dec 2021 04:43:41: #2 alternative fragment length(s) may be 145 bps INFO @ Thu, 09 Dec 2021 04:43:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.20_model.r WARNING @ Thu, 09 Dec 2021 04:43:41: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:43:41: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Thu, 09 Dec 2021 04:43:41: #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 04:43:41: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:43:41: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (388 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:43:54: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:44:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:44:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:44:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX11322244/SRX11322244.20_summits.bed INFO @ Thu, 09 Dec 2021 04:44:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (252 records, 4 fields): 1 millis CompletedMACS2peakCalling