Job ID = 6366196 SRX = SRX065721 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:37:36 prefetch.2.10.7: 1) Downloading 'SRR217427'... 2020-06-15T22:37:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:38:27 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:38:28 prefetch.2.10.7: 'SRR217427' is valid 2020-06-15T22:38:28 prefetch.2.10.7: 1) 'SRR217427' was downloaded successfully Read 9517145 spots for SRR217427/SRR217427.sra Written 9517145 spots for SRR217427/SRR217427.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: 00:01:04 9517145 reads; of these: 9517145 (100.00%) were unpaired; of these: 4764696 (50.06%) aligned 0 times 3938861 (41.39%) aligned exactly 1 time 813588 (8.55%) aligned >1 times 49.94% overall alignment rate Time searching: 00:01:04 Overall time: 00:01:04 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_rmdupse_core] 608304 / 4752449 = 0.1280 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 @ Tue, 16 Jun 2020 07:41:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.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, 16 Jun 2020 07:41:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:41:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:41:25: 1000000 INFO @ Tue, 16 Jun 2020 07:41:31: 2000000 INFO @ Tue, 16 Jun 2020 07:41:36: 3000000 INFO @ Tue, 16 Jun 2020 07:41:41: 4000000 INFO @ Tue, 16 Jun 2020 07:41:41: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:41:41: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:41:41: #1 total tags in treatment: 4144145 INFO @ Tue, 16 Jun 2020 07:41:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:41:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:41:41: #1 tags after filtering in treatment: 4144145 INFO @ Tue, 16 Jun 2020 07:41:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:41:41: #1 finished! INFO @ Tue, 16 Jun 2020 07:41:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:41:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:41:42: #2 number of paired peaks: 594 WARNING @ Tue, 16 Jun 2020 07:41:42: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Tue, 16 Jun 2020 07:41:42: start model_add_line... INFO @ Tue, 16 Jun 2020 07:41:42: start X-correlation... INFO @ Tue, 16 Jun 2020 07:41:42: end of X-cor INFO @ Tue, 16 Jun 2020 07:41:42: #2 finished! INFO @ Tue, 16 Jun 2020 07:41:42: #2 predicted fragment length is 128 bps INFO @ Tue, 16 Jun 2020 07:41:42: #2 alternative fragment length(s) may be 128 bps INFO @ Tue, 16 Jun 2020 07:41:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.05_model.r INFO @ Tue, 16 Jun 2020 07:41:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:41:42: #3 Pre-compute pvalue-qvalue table... 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 @ Tue, 16 Jun 2020 07:41:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.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, 16 Jun 2020 07:41:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:41:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:41:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:41:55: 1000000 INFO @ Tue, 16 Jun 2020 07:41:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:41:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:41:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.05_summits.bed INFO @ Tue, 16 Jun 2020 07:41:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (854 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:42:00: 2000000 INFO @ Tue, 16 Jun 2020 07:42:05: 3000000 INFO @ Tue, 16 Jun 2020 07:42:11: 4000000 INFO @ Tue, 16 Jun 2020 07:42:11: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:42:11: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:42:11: #1 total tags in treatment: 4144145 INFO @ Tue, 16 Jun 2020 07:42:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:42:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:42:11: #1 tags after filtering in treatment: 4144145 INFO @ Tue, 16 Jun 2020 07:42:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:42:11: #1 finished! INFO @ Tue, 16 Jun 2020 07:42:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:42:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:42:12: #2 number of paired peaks: 594 WARNING @ Tue, 16 Jun 2020 07:42:12: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Tue, 16 Jun 2020 07:42:12: start model_add_line... INFO @ Tue, 16 Jun 2020 07:42:12: start X-correlation... INFO @ Tue, 16 Jun 2020 07:42:12: end of X-cor INFO @ Tue, 16 Jun 2020 07:42:12: #2 finished! INFO @ Tue, 16 Jun 2020 07:42:12: #2 predicted fragment length is 128 bps INFO @ Tue, 16 Jun 2020 07:42:12: #2 alternative fragment length(s) may be 128 bps INFO @ Tue, 16 Jun 2020 07:42:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.10_model.r INFO @ Tue, 16 Jun 2020 07:42:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:42:12: #3 Pre-compute pvalue-qvalue table... 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 @ Tue, 16 Jun 2020 07:42:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.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, 16 Jun 2020 07:42:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:42:25: 1000000 INFO @ Tue, 16 Jun 2020 07:42:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:42:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:42:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.10_summits.bed INFO @ Tue, 16 Jun 2020 07:42:26: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (550 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:42:31: 2000000 INFO @ Tue, 16 Jun 2020 07:42:36: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:42:41: 4000000 INFO @ Tue, 16 Jun 2020 07:42:42: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:42:42: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:42:42: #1 total tags in treatment: 4144145 INFO @ Tue, 16 Jun 2020 07:42:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:42:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:42:42: #1 tags after filtering in treatment: 4144145 INFO @ Tue, 16 Jun 2020 07:42:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:42:42: #1 finished! INFO @ Tue, 16 Jun 2020 07:42:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:42:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:42:42: #2 number of paired peaks: 594 WARNING @ Tue, 16 Jun 2020 07:42:42: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Tue, 16 Jun 2020 07:42:42: start model_add_line... INFO @ Tue, 16 Jun 2020 07:42:42: start X-correlation... INFO @ Tue, 16 Jun 2020 07:42:42: end of X-cor INFO @ Tue, 16 Jun 2020 07:42:42: #2 finished! INFO @ Tue, 16 Jun 2020 07:42:42: #2 predicted fragment length is 128 bps INFO @ Tue, 16 Jun 2020 07:42:42: #2 alternative fragment length(s) may be 128 bps INFO @ Tue, 16 Jun 2020 07:42:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.20_model.r INFO @ Tue, 16 Jun 2020 07:42:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:42:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:42:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:42:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:42:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:42:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065721/SRX065721.20_summits.bed INFO @ Tue, 16 Jun 2020 07:42:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (315 records, 4 fields): 2 millis CompletedMACS2peakCalling