Job ID = 6366665 SRX = SRX2202776 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:52:11 prefetch.2.10.7: 1) Downloading 'SRR4319282'... 2020-06-15T22:52:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:53:02 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:53:03 prefetch.2.10.7: 'SRR4319282' is valid 2020-06-15T22:53:03 prefetch.2.10.7: 1) 'SRR4319282' was downloaded successfully 2020-06-15T22:53:36 prefetch.2.10.7: 'SRR4319282' has 6 unresolved dependencies 2020-06-15T22:53:36 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-15T22:53:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:53:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:53:52 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:53:52 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.4?vdb-ctx=refseq'... 2020-06-15T22:53:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:54:08 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:54:08 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:54:08 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.3?vdb-ctx=refseq'... 2020-06-15T22:54:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:54:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:54:24 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.3?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:54:24 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.3?vdb-ctx=refseq'... 2020-06-15T22:54:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:54:41 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:54:41 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.3?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:54:41 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.4?vdb-ctx=refseq'... 2020-06-15T22:54:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:54:58 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:54:58 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:54:58 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.4?vdb-ctx=refseq'... 2020-06-15T22:54:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:55:13 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:55:13 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.4?vdb-ctx=refseq' was downloaded successfully Read 16007623 spots for SRR4319282/SRR4319282.sra Written 16007623 spots for SRR4319282/SRR4319282.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: 00:03:10 16007623 reads; of these: 16007623 (100.00%) were unpaired; of these: 3803888 (23.76%) aligned 0 times 7469051 (46.66%) aligned exactly 1 time 4734684 (29.58%) aligned >1 times 76.24% overall alignment rate Time searching: 00:03:10 Overall time: 00:03:10 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 8 files... [bam_rmdupse_core] 3395844 / 12203735 = 0.2783 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 08:02:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.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 08:02:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:17: 1000000 INFO @ Tue, 16 Jun 2020 08:02:22: 2000000 INFO @ Tue, 16 Jun 2020 08:02:28: 3000000 INFO @ Tue, 16 Jun 2020 08:02:33: 4000000 INFO @ Tue, 16 Jun 2020 08:02:38: 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 08:02:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.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 08:02:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:44: 6000000 INFO @ Tue, 16 Jun 2020 08:02:48: 1000000 INFO @ Tue, 16 Jun 2020 08:02:49: 7000000 INFO @ Tue, 16 Jun 2020 08:02:54: 2000000 INFO @ Tue, 16 Jun 2020 08:02:55: 8000000 INFO @ Tue, 16 Jun 2020 08:03:00: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:03:00: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:03:00: #1 total tags in treatment: 8807891 INFO @ Tue, 16 Jun 2020 08:03:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:00: #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 08:03:00: 3000000 INFO @ Tue, 16 Jun 2020 08:03:00: #1 tags after filtering in treatment: 8807891 INFO @ Tue, 16 Jun 2020 08:03:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:01: #2 number of paired peaks: 2322 INFO @ Tue, 16 Jun 2020 08:03:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:01: #2 predicted fragment length is 114 bps INFO @ Tue, 16 Jun 2020 08:03:01: #2 alternative fragment length(s) may be 3,114 bps INFO @ Tue, 16 Jun 2020 08:03:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.05_model.r INFO @ Tue, 16 Jun 2020 08:03:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:03:06: 4000000 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 08:03:11: 5000000 INFO @ Tue, 16 Jun 2020 08:03:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.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 08:03:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:17: 6000000 INFO @ Tue, 16 Jun 2020 08:03:18: 1000000 INFO @ Tue, 16 Jun 2020 08:03:22: 7000000 INFO @ Tue, 16 Jun 2020 08:03:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:03:23: 2000000 INFO @ Tue, 16 Jun 2020 08:03:28: 8000000 INFO @ Tue, 16 Jun 2020 08:03:29: 3000000 INFO @ Tue, 16 Jun 2020 08:03:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.05_summits.bed INFO @ Tue, 16 Jun 2020 08:03:33: Done! INFO @ Tue, 16 Jun 2020 08:03:33: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:03:33: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:03:33: #1 total tags in treatment: 8807891 INFO @ Tue, 16 Jun 2020 08:03:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4149 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:03:33: #1 tags after filtering in treatment: 8807891 INFO @ Tue, 16 Jun 2020 08:03:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:34: #2 number of paired peaks: 2322 INFO @ Tue, 16 Jun 2020 08:03:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:34: #2 predicted fragment length is 114 bps INFO @ Tue, 16 Jun 2020 08:03:34: #2 alternative fragment length(s) may be 3,114 bps INFO @ Tue, 16 Jun 2020 08:03:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.10_model.r INFO @ Tue, 16 Jun 2020 08:03:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:03:35: 4000000 INFO @ Tue, 16 Jun 2020 08:03:40: 5000000 INFO @ Tue, 16 Jun 2020 08:03:46: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:03:51: 7000000 INFO @ Tue, 16 Jun 2020 08:03:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:03:56: 8000000 INFO @ Tue, 16 Jun 2020 08:04:01: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:04:01: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:04:01: #1 total tags in treatment: 8807891 INFO @ Tue, 16 Jun 2020 08:04:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:01: #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 08:04:01: #1 tags after filtering in treatment: 8807891 INFO @ Tue, 16 Jun 2020 08:04:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:02: #2 number of paired peaks: 2322 INFO @ Tue, 16 Jun 2020 08:04:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:02: #2 predicted fragment length is 114 bps INFO @ Tue, 16 Jun 2020 08:04:02: #2 alternative fragment length(s) may be 3,114 bps INFO @ Tue, 16 Jun 2020 08:04:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.20_model.r INFO @ Tue, 16 Jun 2020 08:04:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.10_summits.bed INFO @ Tue, 16 Jun 2020 08:04:07: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1950 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:04:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202776/SRX2202776.20_summits.bed INFO @ Tue, 16 Jun 2020 08:04:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (735 records, 4 fields): 2 millis CompletedMACS2peakCalling