Job ID = 6508013 SRX = SRX747304 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:28:33 prefetch.2.10.7: 1) Downloading 'SRR1635002'... 2020-06-26T14:28:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:29:44 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:29:45 prefetch.2.10.7: 'SRR1635002' is valid 2020-06-26T14:29:45 prefetch.2.10.7: 1) 'SRR1635002' was downloaded successfully 2020-06-26T14:30:18 prefetch.2.10.7: 'SRR1635002' has 6 unresolved dependencies 2020-06-26T14:30:18 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-26T14:30:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:30:34 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:30:34 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:30:34 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.4?vdb-ctx=refseq'... 2020-06-26T14:30:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:30:50 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:30:51 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:30:51 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.3?vdb-ctx=refseq'... 2020-06-26T14:30:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:31:06 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:31:06 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.3?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:31:06 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.3?vdb-ctx=refseq'... 2020-06-26T14:31:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:31:23 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:31:23 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.3?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:31:23 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.4?vdb-ctx=refseq'... 2020-06-26T14:31:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:31:39 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:31:39 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:31:39 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.4?vdb-ctx=refseq'... 2020-06-26T14:31:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:31:56 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:31:56 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: 00:02:39 23980098 reads; of these: 23980098 (100.00%) were unpaired; of these: 8444572 (35.21%) aligned 0 times 13745555 (57.32%) aligned exactly 1 time 1789971 (7.46%) aligned >1 times 64.79% overall alignment rate Time searching: 00:02:39 Overall time: 00:02:39 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] 6610000 / 15535526 = 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 23:38:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX747304/SRX747304.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX747304/SRX747304.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX747304/SRX747304.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 23:38:38: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:38:38: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:38:45: 1000000 INFO @ Fri, 26 Jun 2020 23:38:52: 2000000 INFO @ Fri, 26 Jun 2020 23:38:58: 3000000 INFO @ Fri, 26 Jun 2020 23:39:05: 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 23:39:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX747304/SRX747304.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX747304/SRX747304.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX747304/SRX747304.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 23:39:08: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:39:08: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:39:13: 5000000 INFO @ Fri, 26 Jun 2020 23:39:15: 1000000 INFO @ Fri, 26 Jun 2020 23:39:20: 6000000 INFO @ Fri, 26 Jun 2020 23:39:21: 2000000 INFO @ Fri, 26 Jun 2020 23:39:27: 7000000 INFO @ Fri, 26 Jun 2020 23:39:28: 3000000 INFO @ Fri, 26 Jun 2020 23:39:34: 4000000 INFO @ Fri, 26 Jun 2020 23:39:35: 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 @ Fri, 26 Jun 2020 23:39:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX747304/SRX747304.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX747304/SRX747304.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX747304/SRX747304.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 23:39:38: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:39:38: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:39:41: 5000000 INFO @ Fri, 26 Jun 2020 23:39:41: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:39:41: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:39:41: #1 total tags in treatment: 8925526 INFO @ Fri, 26 Jun 2020 23:39:41: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:39:41: #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 23:39:42: #1 tags after filtering in treatment: 8925526 INFO @ Fri, 26 Jun 2020 23:39:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:39:42: #1 finished! INFO @ Fri, 26 Jun 2020 23:39:42: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:39:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:39:42: #2 number of paired peaks: 3350 INFO @ Fri, 26 Jun 2020 23:39:42: start model_add_line... INFO @ Fri, 26 Jun 2020 23:39:43: start X-correlation... INFO @ Fri, 26 Jun 2020 23:39:43: end of X-cor INFO @ Fri, 26 Jun 2020 23:39:43: #2 finished! INFO @ Fri, 26 Jun 2020 23:39:43: #2 predicted fragment length is 146 bps INFO @ Fri, 26 Jun 2020 23:39:43: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 26 Jun 2020 23:39:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX747304/SRX747304.05_model.r INFO @ Fri, 26 Jun 2020 23:39:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:39:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:39:46: 1000000 INFO @ Fri, 26 Jun 2020 23:39:48: 6000000 INFO @ Fri, 26 Jun 2020 23:39:53: 2000000 INFO @ Fri, 26 Jun 2020 23:39:54: 7000000 INFO @ Fri, 26 Jun 2020 23:40:00: 3000000 INFO @ Fri, 26 Jun 2020 23:40:01: 8000000 INFO @ Fri, 26 Jun 2020 23:40:07: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:40:07: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:40:07: #1 total tags in treatment: 8925526 INFO @ Fri, 26 Jun 2020 23:40:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:40:07: #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 23:40:07: #1 tags after filtering in treatment: 8925526 INFO @ Fri, 26 Jun 2020 23:40:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:40:07: #1 finished! INFO @ Fri, 26 Jun 2020 23:40:07: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:40:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:40:07: 4000000 INFO @ Fri, 26 Jun 2020 23:40:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:40:08: #2 number of paired peaks: 3350 INFO @ Fri, 26 Jun 2020 23:40:08: start model_add_line... INFO @ Fri, 26 Jun 2020 23:40:08: start X-correlation... INFO @ Fri, 26 Jun 2020 23:40:08: end of X-cor INFO @ Fri, 26 Jun 2020 23:40:08: #2 finished! INFO @ Fri, 26 Jun 2020 23:40:08: #2 predicted fragment length is 146 bps INFO @ Fri, 26 Jun 2020 23:40:08: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 26 Jun 2020 23:40:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX747304/SRX747304.10_model.r INFO @ Fri, 26 Jun 2020 23:40:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:40:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:40:14: 5000000 INFO @ Fri, 26 Jun 2020 23:40:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX747304/SRX747304.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:40:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX747304/SRX747304.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:40:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX747304/SRX747304.05_summits.bed INFO @ Fri, 26 Jun 2020 23:40:20: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6486 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:40:21: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:40:27: 7000000 INFO @ Fri, 26 Jun 2020 23:40:30: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:40:34: 8000000 INFO @ Fri, 26 Jun 2020 23:40:40: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:40:40: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:40:40: #1 total tags in treatment: 8925526 INFO @ Fri, 26 Jun 2020 23:40:40: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:40:40: #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 23:40:40: #1 tags after filtering in treatment: 8925526 INFO @ Fri, 26 Jun 2020 23:40:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:40:40: #1 finished! INFO @ Fri, 26 Jun 2020 23:40:40: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:40:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:40:41: #2 number of paired peaks: 3350 INFO @ Fri, 26 Jun 2020 23:40:41: start model_add_line... INFO @ Fri, 26 Jun 2020 23:40:41: start X-correlation... INFO @ Fri, 26 Jun 2020 23:40:41: end of X-cor INFO @ Fri, 26 Jun 2020 23:40:41: #2 finished! INFO @ Fri, 26 Jun 2020 23:40:41: #2 predicted fragment length is 146 bps INFO @ Fri, 26 Jun 2020 23:40:41: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 26 Jun 2020 23:40:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX747304/SRX747304.20_model.r INFO @ Fri, 26 Jun 2020 23:40:41: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:40:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:40:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX747304/SRX747304.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:40:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX747304/SRX747304.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:40:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX747304/SRX747304.10_summits.bed INFO @ Fri, 26 Jun 2020 23:40:41: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5031 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:41:05: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:41:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX747304/SRX747304.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:41:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX747304/SRX747304.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:41:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX747304/SRX747304.20_summits.bed INFO @ Fri, 26 Jun 2020 23:41:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3831 records, 4 fields): 6 millis CompletedMACS2peakCalling