Job ID = 6367016 SRX = SRX2599461 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:21:31 prefetch.2.10.7: 1) Downloading 'SRR5297105'... 2020-06-15T23:21:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:22:15 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:22:16 prefetch.2.10.7: 'SRR5297105' is valid 2020-06-15T23:22:16 prefetch.2.10.7: 1) 'SRR5297105' was downloaded successfully 2020-06-15T23:22:49 prefetch.2.10.7: 'SRR5297105' has 6 unresolved dependencies 2020-06-15T23:22:49 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-15T23:22:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:23:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:23:04 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:23:04 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.4?vdb-ctx=refseq'... 2020-06-15T23:23:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:23:18 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:23:18 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:23:18 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.3?vdb-ctx=refseq'... 2020-06-15T23:23:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:23:34 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:23:34 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.3?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:23:34 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.3?vdb-ctx=refseq'... 2020-06-15T23:23:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:23:51 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:23:51 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.3?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:23:51 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.4?vdb-ctx=refseq'... 2020-06-15T23:23:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:24:07 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:24:07 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:24:07 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.4?vdb-ctx=refseq'... 2020-06-15T23:24:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:24:22 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:24:22 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.4?vdb-ctx=refseq' was downloaded successfully Read 24778030 spots for SRR5297105/SRR5297105.sra Written 24778030 spots for SRR5297105/SRR5297105.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: 00:04:54 24778030 reads; of these: 24778030 (100.00%) were unpaired; of these: 1033516 (4.17%) aligned 0 times 16646551 (67.18%) aligned exactly 1 time 7097963 (28.65%) aligned >1 times 95.83% overall alignment rate Time searching: 00:04:54 Overall time: 00:04:54 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 12 files... [bam_rmdupse_core] 5796190 / 23744514 = 0.2441 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 08:38:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.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 08:38:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:38:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:38:17: 1000000 INFO @ Tue, 16 Jun 2020 08:38:24: 2000000 INFO @ Tue, 16 Jun 2020 08:38:30: 3000000 INFO @ Tue, 16 Jun 2020 08:38:37: 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 @ Tue, 16 Jun 2020 08:38:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.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 08:38:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:38:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:38:44: 5000000 INFO @ Tue, 16 Jun 2020 08:38:48: 1000000 INFO @ Tue, 16 Jun 2020 08:38:51: 6000000 INFO @ Tue, 16 Jun 2020 08:38:56: 2000000 INFO @ Tue, 16 Jun 2020 08:38:58: 7000000 INFO @ Tue, 16 Jun 2020 08:39:03: 3000000 INFO @ Tue, 16 Jun 2020 08:39:06: 8000000 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 08:39:10: 4000000 INFO @ Tue, 16 Jun 2020 08:39:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.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 08:39:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:39:14: 9000000 INFO @ Tue, 16 Jun 2020 08:39:18: 5000000 INFO @ Tue, 16 Jun 2020 08:39:19: 1000000 INFO @ Tue, 16 Jun 2020 08:39:22: 10000000 INFO @ Tue, 16 Jun 2020 08:39:26: 6000000 INFO @ Tue, 16 Jun 2020 08:39:26: 2000000 INFO @ Tue, 16 Jun 2020 08:39:30: 11000000 INFO @ Tue, 16 Jun 2020 08:39:34: 7000000 INFO @ Tue, 16 Jun 2020 08:39:34: 3000000 INFO @ Tue, 16 Jun 2020 08:39:37: 12000000 INFO @ Tue, 16 Jun 2020 08:39:42: 4000000 INFO @ Tue, 16 Jun 2020 08:39:42: 8000000 INFO @ Tue, 16 Jun 2020 08:39:45: 13000000 INFO @ Tue, 16 Jun 2020 08:39:50: 5000000 INFO @ Tue, 16 Jun 2020 08:39:50: 9000000 INFO @ Tue, 16 Jun 2020 08:39:53: 14000000 INFO @ Tue, 16 Jun 2020 08:39:58: 6000000 INFO @ Tue, 16 Jun 2020 08:39:58: 10000000 INFO @ Tue, 16 Jun 2020 08:40:01: 15000000 INFO @ Tue, 16 Jun 2020 08:40:06: 7000000 INFO @ Tue, 16 Jun 2020 08:40:07: 11000000 INFO @ Tue, 16 Jun 2020 08:40:09: 16000000 INFO @ Tue, 16 Jun 2020 08:40:13: 8000000 INFO @ Tue, 16 Jun 2020 08:40:14: 12000000 INFO @ Tue, 16 Jun 2020 08:40:17: 17000000 INFO @ Tue, 16 Jun 2020 08:40:21: 9000000 INFO @ Tue, 16 Jun 2020 08:40:22: 13000000 INFO @ Tue, 16 Jun 2020 08:40:24: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:40:24: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:40:24: #1 total tags in treatment: 17948324 INFO @ Tue, 16 Jun 2020 08:40:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:24: #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 08:40:25: #1 tags after filtering in treatment: 17948324 INFO @ Tue, 16 Jun 2020 08:40:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:25: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:26: #2 number of paired peaks: 2488 INFO @ Tue, 16 Jun 2020 08:40:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:26: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 08:40:26: #2 alternative fragment length(s) may be 2,149 bps INFO @ Tue, 16 Jun 2020 08:40:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.05_model.r INFO @ Tue, 16 Jun 2020 08:40:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:40:29: 10000000 INFO @ Tue, 16 Jun 2020 08:40:29: 14000000 INFO @ Tue, 16 Jun 2020 08:40:36: 11000000 INFO @ Tue, 16 Jun 2020 08:40:36: 15000000 INFO @ Tue, 16 Jun 2020 08:40:44: 12000000 INFO @ Tue, 16 Jun 2020 08:40:44: 16000000 INFO @ Tue, 16 Jun 2020 08:40:52: 13000000 INFO @ Tue, 16 Jun 2020 08:40:53: 17000000 INFO @ Tue, 16 Jun 2020 08:41:01: 14000000 INFO @ Tue, 16 Jun 2020 08:41:01: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:41:01: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:41:01: #1 total tags in treatment: 17948324 INFO @ Tue, 16 Jun 2020 08:41:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:01: #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 08:41:01: #1 tags after filtering in treatment: 17948324 INFO @ Tue, 16 Jun 2020 08:41:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:03: #2 number of paired peaks: 2488 INFO @ Tue, 16 Jun 2020 08:41:03: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:03: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:03: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:03: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:03: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 08:41:03: #2 alternative fragment length(s) may be 2,149 bps INFO @ Tue, 16 Jun 2020 08:41:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.10_model.r INFO @ Tue, 16 Jun 2020 08:41:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:41:07: 15000000 INFO @ Tue, 16 Jun 2020 08:41:14: 16000000 INFO @ Tue, 16 Jun 2020 08:41:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:21: 17000000 INFO @ Tue, 16 Jun 2020 08:41:28: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:41:28: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:41:28: #1 total tags in treatment: 17948324 INFO @ Tue, 16 Jun 2020 08:41:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:28: #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 08:41:28: #1 tags after filtering in treatment: 17948324 INFO @ Tue, 16 Jun 2020 08:41:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:28: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:30: #2 number of paired peaks: 2488 INFO @ Tue, 16 Jun 2020 08:41:30: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:30: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:30: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:30: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:30: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 08:41:30: #2 alternative fragment length(s) may be 2,149 bps INFO @ Tue, 16 Jun 2020 08:41:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.20_model.r INFO @ Tue, 16 Jun 2020 08:41:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:41:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.05_summits.bed INFO @ Tue, 16 Jun 2020 08:41:36: Done! pass1 - making usageList (7 chroms): 8 millis pass2 - checking and writing primary data (4585 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:41:53: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:42:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.10_summits.bed INFO @ Tue, 16 Jun 2020 08:42:09: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2212 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:42:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:42:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2599461/SRX2599461.20_summits.bed INFO @ Tue, 16 Jun 2020 08:42:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (708 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。