Job ID = 6497560 SRX = SRX743643 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:22:14 prefetch.2.10.7: 1) Downloading 'SRR1630858'... 2020-06-25T22:22:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:24:43 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:24:43 prefetch.2.10.7: 1) 'SRR1630858' was downloaded successfully Read 15651666 spots for SRR1630858/SRR1630858.sra Written 15651666 spots for SRR1630858/SRR1630858.sra 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: 00:03:45 15651666 reads; of these: 15651666 (100.00%) were unpaired; of these: 3599840 (23.00%) aligned 0 times 10436941 (66.68%) aligned exactly 1 time 1614885 (10.32%) aligned >1 times 77.00% overall alignment rate Time searching: 00:03:45 Overall time: 00:03:45 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] 2459327 / 12051826 = 0.2041 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 07:33:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.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 @ Fri, 26 Jun 2020 07:33:00: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:33:00: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:33:07: 1000000 INFO @ Fri, 26 Jun 2020 07:33:13: 2000000 INFO @ Fri, 26 Jun 2020 07:33:19: 3000000 INFO @ Fri, 26 Jun 2020 07:33:24: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 07:33:30: 5000000 INFO @ Fri, 26 Jun 2020 07:33:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.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 @ Fri, 26 Jun 2020 07:33:35: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:33:35: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:33:37: 6000000 INFO @ Fri, 26 Jun 2020 07:33:41: 1000000 INFO @ Fri, 26 Jun 2020 07:33:43: 7000000 INFO @ Fri, 26 Jun 2020 07:33:47: 2000000 INFO @ Fri, 26 Jun 2020 07:33:49: 8000000 INFO @ Fri, 26 Jun 2020 07:33:53: 3000000 INFO @ Fri, 26 Jun 2020 07:33:55: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 07:33:59: 4000000 INFO @ Fri, 26 Jun 2020 07:33:59: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 07:33:59: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 07:33:59: #1 total tags in treatment: 9592499 INFO @ Fri, 26 Jun 2020 07:33:59: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:33:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:33:59: #1 tags after filtering in treatment: 9592499 INFO @ Fri, 26 Jun 2020 07:33:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:33:59: #1 finished! INFO @ Fri, 26 Jun 2020 07:33:59: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:33:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:34:00: #2 number of paired peaks: 868 WARNING @ Fri, 26 Jun 2020 07:34:00: Fewer paired peaks (868) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 868 pairs to build model! INFO @ Fri, 26 Jun 2020 07:34:00: start model_add_line... INFO @ Fri, 26 Jun 2020 07:34:00: start X-correlation... INFO @ Fri, 26 Jun 2020 07:34:00: end of X-cor INFO @ Fri, 26 Jun 2020 07:34:00: #2 finished! INFO @ Fri, 26 Jun 2020 07:34:00: #2 predicted fragment length is 117 bps INFO @ Fri, 26 Jun 2020 07:34:00: #2 alternative fragment length(s) may be 4,117 bps INFO @ Fri, 26 Jun 2020 07:34:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.05_model.r INFO @ Fri, 26 Jun 2020 07:34:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:34:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:34:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.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 @ Fri, 26 Jun 2020 07:34:00: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:34:00: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:34:05: 5000000 INFO @ Fri, 26 Jun 2020 07:34:07: 1000000 INFO @ Fri, 26 Jun 2020 07:34:11: 6000000 INFO @ Fri, 26 Jun 2020 07:34:13: 2000000 INFO @ Fri, 26 Jun 2020 07:34:17: 7000000 INFO @ Fri, 26 Jun 2020 07:34:19: 3000000 INFO @ Fri, 26 Jun 2020 07:34:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:34:24: 8000000 INFO @ Fri, 26 Jun 2020 07:34:25: 4000000 INFO @ Fri, 26 Jun 2020 07:34:30: 9000000 INFO @ Fri, 26 Jun 2020 07:34:31: 5000000 INFO @ Fri, 26 Jun 2020 07:34:34: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 07:34:34: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 07:34:34: #1 total tags in treatment: 9592499 INFO @ Fri, 26 Jun 2020 07:34:34: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:34:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:34:34: #1 tags after filtering in treatment: 9592499 INFO @ Fri, 26 Jun 2020 07:34:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:34:34: #1 finished! INFO @ Fri, 26 Jun 2020 07:34:34: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:34:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:34:35: #2 number of paired peaks: 868 WARNING @ Fri, 26 Jun 2020 07:34:35: Fewer paired peaks (868) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 868 pairs to build model! INFO @ Fri, 26 Jun 2020 07:34:35: start model_add_line... INFO @ Fri, 26 Jun 2020 07:34:35: start X-correlation... INFO @ Fri, 26 Jun 2020 07:34:35: end of X-cor INFO @ Fri, 26 Jun 2020 07:34:35: #2 finished! INFO @ Fri, 26 Jun 2020 07:34:35: #2 predicted fragment length is 117 bps INFO @ Fri, 26 Jun 2020 07:34:35: #2 alternative fragment length(s) may be 4,117 bps INFO @ Fri, 26 Jun 2020 07:34:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.10_model.r INFO @ Fri, 26 Jun 2020 07:34:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:34:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:34:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:34:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:34:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.05_summits.bed INFO @ Fri, 26 Jun 2020 07:34:37: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (19106 records, 4 fields): 19 millis INFO @ Fri, 26 Jun 2020 07:34:37: 6000000 CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:34:43: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:34:49: 8000000 INFO @ Fri, 26 Jun 2020 07:34:55: 9000000 INFO @ Fri, 26 Jun 2020 07:34:57: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:34:59: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 07:34:59: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 07:34:59: #1 total tags in treatment: 9592499 INFO @ Fri, 26 Jun 2020 07:34:59: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:34:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:34:59: #1 tags after filtering in treatment: 9592499 INFO @ Fri, 26 Jun 2020 07:34:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:34:59: #1 finished! INFO @ Fri, 26 Jun 2020 07:34:59: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:34:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:35:00: #2 number of paired peaks: 868 WARNING @ Fri, 26 Jun 2020 07:35:00: Fewer paired peaks (868) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 868 pairs to build model! INFO @ Fri, 26 Jun 2020 07:35:00: start model_add_line... INFO @ Fri, 26 Jun 2020 07:35:00: start X-correlation... INFO @ Fri, 26 Jun 2020 07:35:00: end of X-cor INFO @ Fri, 26 Jun 2020 07:35:00: #2 finished! INFO @ Fri, 26 Jun 2020 07:35:00: #2 predicted fragment length is 117 bps INFO @ Fri, 26 Jun 2020 07:35:00: #2 alternative fragment length(s) may be 4,117 bps INFO @ Fri, 26 Jun 2020 07:35:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.20_model.r INFO @ Fri, 26 Jun 2020 07:35:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:35:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:35:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:35:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:35:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.10_summits.bed INFO @ Fri, 26 Jun 2020 07:35:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (8376 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:35:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:35:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:35:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:35:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX743643/SRX743643.20_summits.bed INFO @ Fri, 26 Jun 2020 07:35:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2030 records, 4 fields): 66 millis CompletedMACS2peakCalling