Job ID = 6367697 SRX = SRX395521 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:45:44 prefetch.2.10.7: 1) Downloading 'SRR1054241'... 2020-06-15T23:45:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:46:28 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:46:28 prefetch.2.10.7: 'SRR1054241' is valid 2020-06-15T23:46:28 prefetch.2.10.7: 1) 'SRR1054241' was downloaded successfully Read 7389441 spots for SRR1054241/SRR1054241.sra Written 7389441 spots for SRR1054241/SRR1054241.sra 2020-06-15T23:46:57 prefetch.2.10.7: 1) Downloading 'SRR1054242'... 2020-06-15T23:46:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:54 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:54 prefetch.2.10.7: 'SRR1054242' is valid 2020-06-15T23:47:54 prefetch.2.10.7: 1) 'SRR1054242' was downloaded successfully Read 8170037 spots for SRR1054242/SRR1054242.sra Written 8170037 spots for SRR1054242/SRR1054242.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: 00:01:51 15559478 reads; of these: 15559478 (100.00%) were unpaired; of these: 6462365 (41.53%) aligned 0 times 7441152 (47.82%) aligned exactly 1 time 1655961 (10.64%) aligned >1 times 58.47% overall alignment rate Time searching: 00:01:51 Overall time: 00:01:51 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] 5794115 / 9097113 = 0.6369 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 08:52:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.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 08:52:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:52:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:52:09: 1000000 INFO @ Tue, 16 Jun 2020 08:52:15: 2000000 INFO @ Tue, 16 Jun 2020 08:52:20: 3000000 INFO @ Tue, 16 Jun 2020 08:52:21: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:52:21: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:52:21: #1 total tags in treatment: 3302998 INFO @ Tue, 16 Jun 2020 08:52:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:52:21: #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 08:52:21: #1 tags after filtering in treatment: 3302998 INFO @ Tue, 16 Jun 2020 08:52:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:52:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:52:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:52:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:52:22: #2 number of paired peaks: 1014 INFO @ Tue, 16 Jun 2020 08:52:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:52:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:52:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:52:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:52:22: #2 predicted fragment length is 147 bps INFO @ Tue, 16 Jun 2020 08:52:22: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 16 Jun 2020 08:52:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.05_model.r INFO @ Tue, 16 Jun 2020 08:52:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:52:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:52:30: #3 Call peaks for each chromosome... 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 08:52:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.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 08:52:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:52:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:52:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:52:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:52:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.05_summits.bed INFO @ Tue, 16 Jun 2020 08:52:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2266 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:52:40: 1000000 INFO @ Tue, 16 Jun 2020 08:52:46: 2000000 INFO @ Tue, 16 Jun 2020 08:52:52: 3000000 INFO @ Tue, 16 Jun 2020 08:52:54: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:52:54: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:52:54: #1 total tags in treatment: 3302998 INFO @ Tue, 16 Jun 2020 08:52:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:52:54: #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 08:52:54: #1 tags after filtering in treatment: 3302998 INFO @ Tue, 16 Jun 2020 08:52:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:52:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:52:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:52:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:52:54: #2 number of paired peaks: 1014 INFO @ Tue, 16 Jun 2020 08:52:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:52:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:52:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:52:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:52:54: #2 predicted fragment length is 147 bps INFO @ Tue, 16 Jun 2020 08:52:54: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 16 Jun 2020 08:52:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.10_model.r INFO @ Tue, 16 Jun 2020 08:52:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:52:54: #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 08:53:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:53:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.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 08:53:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:53:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:53:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:53:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:53:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.10_summits.bed INFO @ Tue, 16 Jun 2020 08:53:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1164 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:53:09: 1000000 INFO @ Tue, 16 Jun 2020 08:53:15: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:53:21: 3000000 INFO @ Tue, 16 Jun 2020 08:53:23: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:53:23: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:53:23: #1 total tags in treatment: 3302998 INFO @ Tue, 16 Jun 2020 08:53:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:53:23: #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 08:53:23: #1 tags after filtering in treatment: 3302998 INFO @ Tue, 16 Jun 2020 08:53:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:53:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:53:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:53:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:53:23: #2 number of paired peaks: 1014 INFO @ Tue, 16 Jun 2020 08:53:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:53:23: start X-correlation... INFO @ Tue, 16 Jun 2020 08:53:23: end of X-cor INFO @ Tue, 16 Jun 2020 08:53:23: #2 finished! INFO @ Tue, 16 Jun 2020 08:53:23: #2 predicted fragment length is 147 bps INFO @ Tue, 16 Jun 2020 08:53:23: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 16 Jun 2020 08:53:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.20_model.r INFO @ Tue, 16 Jun 2020 08:53:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:53:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:53:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:53:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:53:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:53:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395521/SRX395521.20_summits.bed INFO @ Tue, 16 Jun 2020 08:53:36: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (528 records, 4 fields): 1 millis CompletedMACS2peakCalling