Job ID = 6366675 SRX = SRX2202787 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:51:41 prefetch.2.10.7: 1) Downloading 'SRR4319293'... 2020-06-15T22:51:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:52:42 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:52:43 prefetch.2.10.7: 'SRR4319293' is valid 2020-06-15T22:52:43 prefetch.2.10.7: 1) 'SRR4319293' was downloaded successfully 2020-06-15T22:53:16 prefetch.2.10.7: 'SRR4319293' has 6 unresolved dependencies 2020-06-15T22:53:16 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-15T22:53:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:53:34 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:53:34 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:53:34 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.4?vdb-ctx=refseq'... 2020-06-15T22:53:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:53:50 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:53:50 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:53:50 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.3?vdb-ctx=refseq'... 2020-06-15T22:53:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:54:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:54:06 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.3?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:54:06 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.3?vdb-ctx=refseq'... 2020-06-15T22:54:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:54:23 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:54:23 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.3?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:54:23 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.4?vdb-ctx=refseq'... 2020-06-15T22:54:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:54:39 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:54:39 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:54:39 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.4?vdb-ctx=refseq'... 2020-06-15T22:54:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:54:55 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:54:55 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.4?vdb-ctx=refseq' was downloaded successfully Read 20837923 spots for SRR4319293/SRR4319293.sra Written 20837923 spots for SRR4319293/SRR4319293.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: 00:04:19 20837923 reads; of these: 20837923 (100.00%) were unpaired; of these: 3524307 (16.91%) aligned 0 times 10417833 (49.99%) aligned exactly 1 time 6895783 (33.09%) aligned >1 times 83.09% overall alignment rate Time searching: 00:04:19 Overall time: 00:04:19 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] 6053370 / 17313616 = 0.3496 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 08:04:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.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 08:04:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:15: 1000000 INFO @ Tue, 16 Jun 2020 08:04:21: 2000000 INFO @ Tue, 16 Jun 2020 08:04:27: 3000000 INFO @ Tue, 16 Jun 2020 08:04:32: 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 08:04:38: 5000000 INFO @ Tue, 16 Jun 2020 08:04:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.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 08:04:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:44: 6000000 INFO @ Tue, 16 Jun 2020 08:04:46: 1000000 INFO @ Tue, 16 Jun 2020 08:04:51: 7000000 INFO @ Tue, 16 Jun 2020 08:04:52: 2000000 INFO @ Tue, 16 Jun 2020 08:04:57: 8000000 INFO @ Tue, 16 Jun 2020 08:04:59: 3000000 INFO @ Tue, 16 Jun 2020 08:05:04: 9000000 INFO @ Tue, 16 Jun 2020 08:05:05: 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 08:05:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.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 08:05:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:10: 10000000 INFO @ Tue, 16 Jun 2020 08:05:12: 5000000 INFO @ Tue, 16 Jun 2020 08:05:16: 1000000 INFO @ Tue, 16 Jun 2020 08:05:17: 11000000 INFO @ Tue, 16 Jun 2020 08:05:19: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:05:19: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:05:19: #1 total tags in treatment: 11260246 INFO @ Tue, 16 Jun 2020 08:05:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:19: #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 08:05:19: 6000000 INFO @ Tue, 16 Jun 2020 08:05:19: #1 tags after filtering in treatment: 11260246 INFO @ Tue, 16 Jun 2020 08:05:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:05:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:05:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:05:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:05:20: #2 number of paired peaks: 1639 INFO @ Tue, 16 Jun 2020 08:05:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:05:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:05:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:05:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:05:20: #2 predicted fragment length is 136 bps INFO @ Tue, 16 Jun 2020 08:05:20: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 16 Jun 2020 08:05:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.05_model.r INFO @ Tue, 16 Jun 2020 08:05:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:05:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:05:23: 2000000 INFO @ Tue, 16 Jun 2020 08:05:25: 7000000 INFO @ Tue, 16 Jun 2020 08:05:30: 3000000 INFO @ Tue, 16 Jun 2020 08:05:32: 8000000 INFO @ Tue, 16 Jun 2020 08:05:37: 4000000 INFO @ Tue, 16 Jun 2020 08:05:39: 9000000 INFO @ Tue, 16 Jun 2020 08:05:43: 5000000 INFO @ Tue, 16 Jun 2020 08:05:45: 10000000 INFO @ Tue, 16 Jun 2020 08:05:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:05:50: 6000000 INFO @ Tue, 16 Jun 2020 08:05:52: 11000000 INFO @ Tue, 16 Jun 2020 08:05:53: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:05:53: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:05:53: #1 total tags in treatment: 11260246 INFO @ Tue, 16 Jun 2020 08:05:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:53: #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 08:05:54: #1 tags after filtering in treatment: 11260246 INFO @ Tue, 16 Jun 2020 08:05:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:05:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:05:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:05:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:05:55: #2 number of paired peaks: 1639 INFO @ Tue, 16 Jun 2020 08:05:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:05:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:05:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:05:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:05:55: #2 predicted fragment length is 136 bps INFO @ Tue, 16 Jun 2020 08:05:55: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 16 Jun 2020 08:05:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.10_model.r INFO @ Tue, 16 Jun 2020 08:05:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:05:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:05:56: 7000000 INFO @ Tue, 16 Jun 2020 08:06:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.05_summits.bed INFO @ Tue, 16 Jun 2020 08:06:01: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6831 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:06:02: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:06:08: 9000000 INFO @ Tue, 16 Jun 2020 08:06:14: 10000000 INFO @ Tue, 16 Jun 2020 08:06:20: 11000000 INFO @ Tue, 16 Jun 2020 08:06:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:06:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:06:21: #1 total tags in treatment: 11260246 INFO @ Tue, 16 Jun 2020 08:06:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:21: #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 08:06:22: #1 tags after filtering in treatment: 11260246 INFO @ Tue, 16 Jun 2020 08:06:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:22: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:23: #2 number of paired peaks: 1639 INFO @ Tue, 16 Jun 2020 08:06:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:23: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:23: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:23: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:23: #2 predicted fragment length is 136 bps INFO @ Tue, 16 Jun 2020 08:06:23: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 16 Jun 2020 08:06:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.20_model.r INFO @ Tue, 16 Jun 2020 08:06:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:06:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.10_summits.bed INFO @ Tue, 16 Jun 2020 08:06:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4361 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:06:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202787/SRX2202787.20_summits.bed INFO @ Tue, 16 Jun 2020 08:07:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2623 records, 4 fields): 5 millis CompletedMACS2peakCalling