Job ID = 6497578 SRX = SRX747304 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:07:04 prefetch.2.10.7: 1) Downloading 'SRR1635002'... 2020-06-25T22:07:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:10:08 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:10:09 prefetch.2.10.7: 'SRR1635002' is valid 2020-06-25T22:10:09 prefetch.2.10.7: 1) 'SRR1635002' was downloaded successfully 2020-06-25T22:10:42 prefetch.2.10.7: 'SRR1635002' has 6 unresolved dependencies 2020-06-25T22:10:42 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-25T22:10:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:10:57 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:10:57 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.4?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:10:57 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.4?vdb-ctx=refseq'... 2020-06-25T22:11:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:11:25 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:11:25 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.4?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:11:25 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.3?vdb-ctx=refseq'... 2020-06-25T22:11:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:11:40 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:11:40 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.3?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:11:40 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.3?vdb-ctx=refseq'... 2020-06-25T22:11:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:11:59 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:11:59 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.3?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:11:59 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.4?vdb-ctx=refseq'... 2020-06-25T22:11:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:12:15 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:12:15 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.4?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:12:15 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.4?vdb-ctx=refseq'... 2020-06-25T22:12:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:12:33 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:12:33 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.4?vdb-ctx=refseq' was downloaded successfully Read 23980098 spots for SRR1635002/SRR1635002.sra Written 23980098 spots for SRR1635002/SRR1635002.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: 00:02:38 23980098 reads; of these: 23980098 (100.00%) were unpaired; of these: 8445531 (35.22%) aligned 0 times 13744715 (57.32%) aligned exactly 1 time 1789852 (7.46%) aligned >1 times 64.78% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 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] 6609548 / 15534567 = 0.4255 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 @ Fri, 26 Jun 2020 07:19:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.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 @ Fri, 26 Jun 2020 07:19:52: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:19:52: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:19:58: 1000000 INFO @ Fri, 26 Jun 2020 07:20:04: 2000000 INFO @ Fri, 26 Jun 2020 07:20:09: 3000000 INFO @ Fri, 26 Jun 2020 07:20:15: 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 @ Fri, 26 Jun 2020 07:20:21: 5000000 INFO @ Fri, 26 Jun 2020 07:20:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.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 @ Fri, 26 Jun 2020 07:20:22: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:20:22: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:20:27: 6000000 INFO @ Fri, 26 Jun 2020 07:20:28: 1000000 INFO @ Fri, 26 Jun 2020 07:20:33: 7000000 INFO @ Fri, 26 Jun 2020 07:20:34: 2000000 INFO @ Fri, 26 Jun 2020 07:20:39: 8000000 INFO @ Fri, 26 Jun 2020 07:20:40: 3000000 INFO @ Fri, 26 Jun 2020 07:20:45: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:20:45: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:20:45: #1 total tags in treatment: 8925019 INFO @ Fri, 26 Jun 2020 07:20:45: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:20:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:20:45: #1 tags after filtering in treatment: 8925019 INFO @ Fri, 26 Jun 2020 07:20:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:20:45: #1 finished! INFO @ Fri, 26 Jun 2020 07:20:45: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:20:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:20:46: 4000000 INFO @ Fri, 26 Jun 2020 07:20:46: #2 number of paired peaks: 3353 INFO @ Fri, 26 Jun 2020 07:20:46: start model_add_line... INFO @ Fri, 26 Jun 2020 07:20:46: start X-correlation... INFO @ Fri, 26 Jun 2020 07:20:46: end of X-cor INFO @ Fri, 26 Jun 2020 07:20:46: #2 finished! INFO @ Fri, 26 Jun 2020 07:20:46: #2 predicted fragment length is 146 bps INFO @ Fri, 26 Jun 2020 07:20:46: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 26 Jun 2020 07:20:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.05_model.r INFO @ Fri, 26 Jun 2020 07:20:46: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:20:46: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 07:20:52: 5000000 INFO @ Fri, 26 Jun 2020 07:20:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.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 @ Fri, 26 Jun 2020 07:20:52: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:20:52: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:20:58: 6000000 INFO @ Fri, 26 Jun 2020 07:20:58: 1000000 INFO @ Fri, 26 Jun 2020 07:21:03: 7000000 INFO @ Fri, 26 Jun 2020 07:21:05: 2000000 INFO @ Fri, 26 Jun 2020 07:21:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:21:09: 8000000 INFO @ Fri, 26 Jun 2020 07:21:11: 3000000 INFO @ Fri, 26 Jun 2020 07:21:15: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:21:15: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:21:15: #1 total tags in treatment: 8925019 INFO @ Fri, 26 Jun 2020 07:21:15: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:21:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:21:15: #1 tags after filtering in treatment: 8925019 INFO @ Fri, 26 Jun 2020 07:21:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:21:15: #1 finished! INFO @ Fri, 26 Jun 2020 07:21:15: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:21:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:21:16: #2 number of paired peaks: 3353 INFO @ Fri, 26 Jun 2020 07:21:16: start model_add_line... INFO @ Fri, 26 Jun 2020 07:21:16: start X-correlation... INFO @ Fri, 26 Jun 2020 07:21:16: end of X-cor INFO @ Fri, 26 Jun 2020 07:21:16: #2 finished! INFO @ Fri, 26 Jun 2020 07:21:16: #2 predicted fragment length is 146 bps INFO @ Fri, 26 Jun 2020 07:21:16: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 26 Jun 2020 07:21:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.10_model.r INFO @ Fri, 26 Jun 2020 07:21:16: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:21:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:21:17: 4000000 INFO @ Fri, 26 Jun 2020 07:21:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:21:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:21:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.05_summits.bed INFO @ Fri, 26 Jun 2020 07:21:18: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6482 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:21:24: 5000000 INFO @ Fri, 26 Jun 2020 07:21:30: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:21:36: 7000000 INFO @ Fri, 26 Jun 2020 07:21:37: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:21:42: 8000000 INFO @ Fri, 26 Jun 2020 07:21:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:21:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:21:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.10_summits.bed INFO @ Fri, 26 Jun 2020 07:21:47: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5032 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:21:48: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:21:48: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:21:48: #1 total tags in treatment: 8925019 INFO @ Fri, 26 Jun 2020 07:21:48: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:21:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:21:48: #1 tags after filtering in treatment: 8925019 INFO @ Fri, 26 Jun 2020 07:21:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:21:48: #1 finished! INFO @ Fri, 26 Jun 2020 07:21:48: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:21:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:21:49: #2 number of paired peaks: 3353 INFO @ Fri, 26 Jun 2020 07:21:49: start model_add_line... INFO @ Fri, 26 Jun 2020 07:21:49: start X-correlation... INFO @ Fri, 26 Jun 2020 07:21:49: end of X-cor INFO @ Fri, 26 Jun 2020 07:21:49: #2 finished! INFO @ Fri, 26 Jun 2020 07:21:49: #2 predicted fragment length is 146 bps INFO @ Fri, 26 Jun 2020 07:21:49: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 26 Jun 2020 07:21:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.20_model.r INFO @ Fri, 26 Jun 2020 07:21:49: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:21:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:22:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:22:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:22:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:22:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX747304/SRX747304.20_summits.bed INFO @ Fri, 26 Jun 2020 07:22:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3830 records, 4 fields): 202 millis CompletedMACS2peakCalling