Job ID = 6367611 SRX = SRX335103 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:27:51 prefetch.2.10.7: 1) Downloading 'SRR952381'... 2020-06-15T23:27:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:29:16 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:29:17 prefetch.2.10.7: 'SRR952381' is valid 2020-06-15T23:29:17 prefetch.2.10.7: 1) 'SRR952381' was downloaded successfully Read 11499142 spots for SRR952381/SRR952381.sra Written 11499142 spots for SRR952381/SRR952381.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: 00:01:55 11499142 reads; of these: 11499142 (100.00%) were unpaired; of these: 180376 (1.57%) aligned 0 times 9899668 (86.09%) aligned exactly 1 time 1419098 (12.34%) aligned >1 times 98.43% overall alignment rate Time searching: 00:01:55 Overall time: 00:01:55 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] 4249754 / 11318766 = 0.3755 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 08:34:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.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 08:34:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:08: 1000000 INFO @ Tue, 16 Jun 2020 08:34:13: 2000000 INFO @ Tue, 16 Jun 2020 08:34:18: 3000000 INFO @ Tue, 16 Jun 2020 08:34:23: 4000000 INFO @ Tue, 16 Jun 2020 08:34:28: 5000000 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 08:34:32: 6000000 INFO @ Tue, 16 Jun 2020 08:34:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.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 08:34:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:38: 7000000 INFO @ Tue, 16 Jun 2020 08:34:38: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:34:38: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:34:38: #1 total tags in treatment: 7069012 INFO @ Tue, 16 Jun 2020 08:34:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:38: #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 08:34:38: #1 tags after filtering in treatment: 7069012 INFO @ Tue, 16 Jun 2020 08:34:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:39: #2 number of paired peaks: 4419 INFO @ Tue, 16 Jun 2020 08:34:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:39: #2 predicted fragment length is 161 bps INFO @ Tue, 16 Jun 2020 08:34:39: #2 alternative fragment length(s) may be 161 bps INFO @ Tue, 16 Jun 2020 08:34:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.05_model.r INFO @ Tue, 16 Jun 2020 08:34:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:39: 1000000 INFO @ Tue, 16 Jun 2020 08:34:44: 2000000 INFO @ Tue, 16 Jun 2020 08:34:49: 3000000 INFO @ Tue, 16 Jun 2020 08:34:54: 4000000 INFO @ Tue, 16 Jun 2020 08:34:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:59: 5000000 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 08:35:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.05_summits.bed INFO @ Tue, 16 Jun 2020 08:35:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5724 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:35:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.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 08:35:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:04: 6000000 INFO @ Tue, 16 Jun 2020 08:35:10: 7000000 INFO @ Tue, 16 Jun 2020 08:35:10: 1000000 INFO @ Tue, 16 Jun 2020 08:35:10: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:35:10: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:35:10: #1 total tags in treatment: 7069012 INFO @ Tue, 16 Jun 2020 08:35:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:10: #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 08:35:10: #1 tags after filtering in treatment: 7069012 INFO @ Tue, 16 Jun 2020 08:35:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:10: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:11: #2 number of paired peaks: 4419 INFO @ Tue, 16 Jun 2020 08:35:11: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:11: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:11: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:11: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:11: #2 predicted fragment length is 161 bps INFO @ Tue, 16 Jun 2020 08:35:11: #2 alternative fragment length(s) may be 161 bps INFO @ Tue, 16 Jun 2020 08:35:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.10_model.r INFO @ Tue, 16 Jun 2020 08:35:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:35:16: 2000000 INFO @ Tue, 16 Jun 2020 08:35:21: 3000000 INFO @ Tue, 16 Jun 2020 08:35:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:35:27: 4000000 INFO @ Tue, 16 Jun 2020 08:35:33: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:35:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.10_summits.bed INFO @ Tue, 16 Jun 2020 08:35:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4792 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:35:38: 6000000 INFO @ Tue, 16 Jun 2020 08:35:44: 7000000 INFO @ Tue, 16 Jun 2020 08:35:44: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:35:44: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:35:44: #1 total tags in treatment: 7069012 INFO @ Tue, 16 Jun 2020 08:35:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:44: #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 08:35:45: #1 tags after filtering in treatment: 7069012 INFO @ Tue, 16 Jun 2020 08:35:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:45: #2 number of paired peaks: 4419 INFO @ Tue, 16 Jun 2020 08:35:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:45: #2 predicted fragment length is 161 bps INFO @ Tue, 16 Jun 2020 08:35:45: #2 alternative fragment length(s) may be 161 bps INFO @ Tue, 16 Jun 2020 08:35:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.20_model.r INFO @ Tue, 16 Jun 2020 08:35:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:36:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX335103/SRX335103.20_summits.bed INFO @ Tue, 16 Jun 2020 08:36:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3840 records, 4 fields): 5 millis CompletedMACS2peakCalling