Job ID = 6497570 SRX = SRX747296 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:56:43 prefetch.2.10.7: 1) Downloading 'SRR1634994'... 2020-06-25T22:56:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:57:24 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:57:24 prefetch.2.10.7: 'SRR1634994' is valid 2020-06-25T22:57:24 prefetch.2.10.7: 1) 'SRR1634994' was downloaded successfully 2020-06-25T22:57:57 prefetch.2.10.7: 'SRR1634994' has 6 unresolved dependencies 2020-06-25T22:57:57 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-25T22:57:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:58:08 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:58:08 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.4?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:58:08 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.4?vdb-ctx=refseq'... 2020-06-25T22:58:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:58:25 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:58:25 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.4?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:58:25 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.3?vdb-ctx=refseq'... 2020-06-25T22:58:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:58:40 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:58:40 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.3?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:58:40 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.3?vdb-ctx=refseq'... 2020-06-25T22:58:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:58:57 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:58:57 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.3?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:58:57 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.4?vdb-ctx=refseq'... 2020-06-25T22:58:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:59:14 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:59:14 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.4?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:59:14 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.4?vdb-ctx=refseq'... 2020-06-25T22:59:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:59:31 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:59:31 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.4?vdb-ctx=refseq' was downloaded successfully Read 16294611 spots for SRR1634994/SRR1634994.sra Written 16294611 spots for SRR1634994/SRR1634994.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: 00:02:35 16294611 reads; of these: 16294611 (100.00%) were unpaired; of these: 483557 (2.97%) aligned 0 times 13888031 (85.23%) aligned exactly 1 time 1923023 (11.80%) aligned >1 times 97.03% overall alignment rate Time searching: 00:02:35 Overall time: 00:02:35 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] 2368176 / 15811054 = 0.1498 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 08:06:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.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 08:06:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:06:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:06:32: 1000000 INFO @ Fri, 26 Jun 2020 08:06:40: 2000000 INFO @ Fri, 26 Jun 2020 08:06:47: 3000000 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 08:06:54: 4000000 INFO @ Fri, 26 Jun 2020 08:06:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.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 08:06:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:06:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:07:02: 5000000 INFO @ Fri, 26 Jun 2020 08:07:03: 1000000 INFO @ Fri, 26 Jun 2020 08:07:09: 6000000 INFO @ Fri, 26 Jun 2020 08:07:11: 2000000 INFO @ Fri, 26 Jun 2020 08:07:17: 7000000 INFO @ Fri, 26 Jun 2020 08:07:19: 3000000 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 08:07:25: 8000000 INFO @ Fri, 26 Jun 2020 08:07:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.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 08:07:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:07:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:07:26: 4000000 INFO @ Fri, 26 Jun 2020 08:07:33: 9000000 INFO @ Fri, 26 Jun 2020 08:07:34: 1000000 INFO @ Fri, 26 Jun 2020 08:07:34: 5000000 INFO @ Fri, 26 Jun 2020 08:07:40: 10000000 INFO @ Fri, 26 Jun 2020 08:07:41: 2000000 INFO @ Fri, 26 Jun 2020 08:07:42: 6000000 INFO @ Fri, 26 Jun 2020 08:07:48: 11000000 INFO @ Fri, 26 Jun 2020 08:07:49: 3000000 INFO @ Fri, 26 Jun 2020 08:07:50: 7000000 INFO @ Fri, 26 Jun 2020 08:07:56: 12000000 INFO @ Fri, 26 Jun 2020 08:07:57: 4000000 INFO @ Fri, 26 Jun 2020 08:07:57: 8000000 INFO @ Fri, 26 Jun 2020 08:08:03: 13000000 INFO @ Fri, 26 Jun 2020 08:08:04: 5000000 INFO @ Fri, 26 Jun 2020 08:08:05: 9000000 INFO @ Fri, 26 Jun 2020 08:08:06: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 08:08:06: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 08:08:06: #1 total tags in treatment: 13442878 INFO @ Fri, 26 Jun 2020 08:08:06: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:08:06: #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 08:08:06: #1 tags after filtering in treatment: 13442878 INFO @ Fri, 26 Jun 2020 08:08:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:08:06: #1 finished! INFO @ Fri, 26 Jun 2020 08:08:06: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:08:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:08:08: #2 number of paired peaks: 1599 INFO @ Fri, 26 Jun 2020 08:08:08: start model_add_line... INFO @ Fri, 26 Jun 2020 08:08:08: start X-correlation... INFO @ Fri, 26 Jun 2020 08:08:08: end of X-cor INFO @ Fri, 26 Jun 2020 08:08:08: #2 finished! INFO @ Fri, 26 Jun 2020 08:08:08: #2 predicted fragment length is 115 bps INFO @ Fri, 26 Jun 2020 08:08:08: #2 alternative fragment length(s) may be 4,115 bps INFO @ Fri, 26 Jun 2020 08:08:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.05_model.r INFO @ Fri, 26 Jun 2020 08:08:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:08:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:08:12: 6000000 INFO @ Fri, 26 Jun 2020 08:08:13: 10000000 INFO @ Fri, 26 Jun 2020 08:08:19: 7000000 INFO @ Fri, 26 Jun 2020 08:08:20: 11000000 INFO @ Fri, 26 Jun 2020 08:08:27: 8000000 INFO @ Fri, 26 Jun 2020 08:08:28: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:08:35: 9000000 INFO @ Fri, 26 Jun 2020 08:08:35: 13000000 INFO @ Fri, 26 Jun 2020 08:08:38: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 08:08:38: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 08:08:38: #1 total tags in treatment: 13442878 INFO @ Fri, 26 Jun 2020 08:08:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:08:38: #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 08:08:38: #1 tags after filtering in treatment: 13442878 INFO @ Fri, 26 Jun 2020 08:08:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:08:38: #1 finished! INFO @ Fri, 26 Jun 2020 08:08:38: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:08:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:08:40: #2 number of paired peaks: 1599 INFO @ Fri, 26 Jun 2020 08:08:40: start model_add_line... INFO @ Fri, 26 Jun 2020 08:08:40: start X-correlation... INFO @ Fri, 26 Jun 2020 08:08:40: end of X-cor INFO @ Fri, 26 Jun 2020 08:08:40: #2 finished! INFO @ Fri, 26 Jun 2020 08:08:40: #2 predicted fragment length is 115 bps INFO @ Fri, 26 Jun 2020 08:08:40: #2 alternative fragment length(s) may be 4,115 bps INFO @ Fri, 26 Jun 2020 08:08:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.10_model.r INFO @ Fri, 26 Jun 2020 08:08:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:08:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:08:42: 10000000 INFO @ Fri, 26 Jun 2020 08:08:43: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:08:49: 11000000 INFO @ Fri, 26 Jun 2020 08:08:56: 12000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:09:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:09:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:09:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.05_summits.bed INFO @ Fri, 26 Jun 2020 08:09:02: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (14954 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:09:03: 13000000 INFO @ Fri, 26 Jun 2020 08:09:06: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 08:09:06: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 08:09:06: #1 total tags in treatment: 13442878 INFO @ Fri, 26 Jun 2020 08:09:06: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:09:06: #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 08:09:06: #1 tags after filtering in treatment: 13442878 INFO @ Fri, 26 Jun 2020 08:09:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:09:06: #1 finished! INFO @ Fri, 26 Jun 2020 08:09:06: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:09:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:09:07: #2 number of paired peaks: 1599 INFO @ Fri, 26 Jun 2020 08:09:07: start model_add_line... INFO @ Fri, 26 Jun 2020 08:09:08: start X-correlation... INFO @ Fri, 26 Jun 2020 08:09:08: end of X-cor INFO @ Fri, 26 Jun 2020 08:09:08: #2 finished! INFO @ Fri, 26 Jun 2020 08:09:08: #2 predicted fragment length is 115 bps INFO @ Fri, 26 Jun 2020 08:09:08: #2 alternative fragment length(s) may be 4,115 bps INFO @ Fri, 26 Jun 2020 08:09:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.20_model.r INFO @ Fri, 26 Jun 2020 08:09:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:09:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:09:15: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:09:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:09:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:09:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.10_summits.bed INFO @ Fri, 26 Jun 2020 08:09:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (8751 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:09:43: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:10:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:10:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:10:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX747296/SRX747296.20_summits.bed INFO @ Fri, 26 Jun 2020 08:10:02: Done! pass1 - making usageList (6 chroms): 5 millis pass2 - checking and writing primary data (3104 records, 4 fields): 4 millis CompletedMACS2peakCalling