Job ID = 6366672 SRX = SRX2202785 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:57:53 prefetch.2.10.7: 1) Downloading 'SRR4319291'... 2020-06-15T22:57:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:58:35 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:58:36 prefetch.2.10.7: 'SRR4319291' is valid 2020-06-15T22:58:36 prefetch.2.10.7: 1) 'SRR4319291' was downloaded successfully 2020-06-15T22:59:08 prefetch.2.10.7: 'SRR4319291' has 6 unresolved dependencies 2020-06-15T22:59:08 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-15T22:59:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:59:25 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:59:25 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:59:25 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.4?vdb-ctx=refseq'... 2020-06-15T22:59:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:59:41 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:59:41 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:59:41 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.3?vdb-ctx=refseq'... 2020-06-15T22:59:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:59:57 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:59:57 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.3?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:59:57 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.3?vdb-ctx=refseq'... 2020-06-15T22:59:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:00:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:00:12 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.3?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:00:12 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.4?vdb-ctx=refseq'... 2020-06-15T23:00:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:00:28 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:00:28 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:00:28 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.4?vdb-ctx=refseq'... 2020-06-15T23:00:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:00:45 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:00:45 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.4?vdb-ctx=refseq' was downloaded successfully Read 22406252 spots for SRR4319291/SRR4319291.sra Written 22406252 spots for SRR4319291/SRR4319291.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: 00:04:07 22406252 reads; of these: 22406252 (100.00%) were unpaired; of these: 2509648 (11.20%) aligned 0 times 14104368 (62.95%) aligned exactly 1 time 5792236 (25.85%) aligned >1 times 88.80% overall alignment rate Time searching: 00:04:07 Overall time: 00:04:07 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] 4915561 / 19896604 = 0.2471 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 08:10:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.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 08:10:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:35: 1000000 INFO @ Tue, 16 Jun 2020 08:10:39: 2000000 INFO @ Tue, 16 Jun 2020 08:10:44: 3000000 INFO @ Tue, 16 Jun 2020 08:10:49: 4000000 INFO @ Tue, 16 Jun 2020 08:10:54: 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 08:10:58: 6000000 INFO @ Tue, 16 Jun 2020 08:11:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.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 08:11:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:11:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:03: 7000000 INFO @ Tue, 16 Jun 2020 08:11:05: 1000000 INFO @ Tue, 16 Jun 2020 08:11:08: 8000000 INFO @ Tue, 16 Jun 2020 08:11:10: 2000000 INFO @ Tue, 16 Jun 2020 08:11:13: 9000000 INFO @ Tue, 16 Jun 2020 08:11:15: 3000000 INFO @ Tue, 16 Jun 2020 08:11:18: 10000000 INFO @ Tue, 16 Jun 2020 08:11:20: 4000000 INFO @ Tue, 16 Jun 2020 08:11:22: 11000000 INFO @ Tue, 16 Jun 2020 08:11:25: 5000000 INFO @ Tue, 16 Jun 2020 08:11:27: 12000000 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 08:11:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.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 08:11:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:11:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:30: 6000000 INFO @ Tue, 16 Jun 2020 08:11:32: 13000000 INFO @ Tue, 16 Jun 2020 08:11:35: 1000000 INFO @ Tue, 16 Jun 2020 08:11:35: 7000000 INFO @ Tue, 16 Jun 2020 08:11:37: 14000000 INFO @ Tue, 16 Jun 2020 08:11:40: 2000000 INFO @ Tue, 16 Jun 2020 08:11:40: 8000000 INFO @ Tue, 16 Jun 2020 08:11:42: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:11:42: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:11:42: #1 total tags in treatment: 14981043 INFO @ Tue, 16 Jun 2020 08:11:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:11:42: #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 08:11:42: #1 tags after filtering in treatment: 14981043 INFO @ Tue, 16 Jun 2020 08:11:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:11:42: #1 finished! INFO @ Tue, 16 Jun 2020 08:11:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:11:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:43: #2 number of paired peaks: 2219 INFO @ Tue, 16 Jun 2020 08:11:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:43: #2 predicted fragment length is 107 bps INFO @ Tue, 16 Jun 2020 08:11:43: #2 alternative fragment length(s) may be 4,107 bps INFO @ Tue, 16 Jun 2020 08:11:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.05_model.r INFO @ Tue, 16 Jun 2020 08:11:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:11:45: 3000000 INFO @ Tue, 16 Jun 2020 08:11:46: 9000000 INFO @ Tue, 16 Jun 2020 08:11:50: 4000000 INFO @ Tue, 16 Jun 2020 08:11:50: 10000000 INFO @ Tue, 16 Jun 2020 08:11:55: 5000000 INFO @ Tue, 16 Jun 2020 08:11:55: 11000000 INFO @ Tue, 16 Jun 2020 08:11:59: 6000000 INFO @ Tue, 16 Jun 2020 08:12:00: 12000000 INFO @ Tue, 16 Jun 2020 08:12:04: 7000000 INFO @ Tue, 16 Jun 2020 08:12:05: 13000000 INFO @ Tue, 16 Jun 2020 08:12:09: 8000000 INFO @ Tue, 16 Jun 2020 08:12:11: 14000000 INFO @ Tue, 16 Jun 2020 08:12:14: 9000000 INFO @ Tue, 16 Jun 2020 08:12:16: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:12:16: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:12:16: #1 total tags in treatment: 14981043 INFO @ Tue, 16 Jun 2020 08:12:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:16: #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 08:12:16: #1 tags after filtering in treatment: 14981043 INFO @ Tue, 16 Jun 2020 08:12:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:12:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:18: #2 number of paired peaks: 2219 INFO @ Tue, 16 Jun 2020 08:12:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:18: #2 predicted fragment length is 107 bps INFO @ Tue, 16 Jun 2020 08:12:18: #2 alternative fragment length(s) may be 4,107 bps INFO @ Tue, 16 Jun 2020 08:12:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.10_model.r INFO @ Tue, 16 Jun 2020 08:12:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:12:19: 10000000 INFO @ Tue, 16 Jun 2020 08:12:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:12:24: 11000000 INFO @ Tue, 16 Jun 2020 08:12:29: 12000000 INFO @ Tue, 16 Jun 2020 08:12:33: 13000000 INFO @ Tue, 16 Jun 2020 08:12:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.05_summits.bed INFO @ Tue, 16 Jun 2020 08:12:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (9987 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:12:38: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:12:43: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:12:43: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:12:43: #1 total tags in treatment: 14981043 INFO @ Tue, 16 Jun 2020 08:12:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:43: #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 08:12:43: #1 tags after filtering in treatment: 14981043 INFO @ Tue, 16 Jun 2020 08:12:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:12:43: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:45: #2 number of paired peaks: 2219 INFO @ Tue, 16 Jun 2020 08:12:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:45: #2 predicted fragment length is 107 bps INFO @ Tue, 16 Jun 2020 08:12:45: #2 alternative fragment length(s) may be 4,107 bps INFO @ Tue, 16 Jun 2020 08:12:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.20_model.r INFO @ Tue, 16 Jun 2020 08:12:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:12:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:13:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:13:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:13:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.10_summits.bed INFO @ Tue, 16 Jun 2020 08:13:11: Done! BigWig に変換しました。 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5368 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:13:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:13:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:13:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:13:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202785/SRX2202785.20_summits.bed INFO @ Tue, 16 Jun 2020 08:13:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2181 records, 4 fields): 3 millis CompletedMACS2peakCalling