Job ID = 6451792 SRX = ERX011412 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T06:53:43 prefetch.2.10.7: 1) Downloading 'ERR031133'... 2020-06-21T06:53:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T06:55:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T06:55:33 prefetch.2.10.7: 'ERR031133' is valid 2020-06-21T06:55:33 prefetch.2.10.7: 1) 'ERR031133' was downloaded successfully 2020-06-21T06:56:25 prefetch.2.10.7: 'ERR031133' has 10 unresolved dependencies 2020-06-21T06:56:25 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.4?vdb-ctx=refseq'... 2020-06-21T06:56:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T06:56:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T06:56:45 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T06:56:45 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.5?vdb-ctx=refseq'... 2020-06-21T06:56:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T06:57:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T06:57:02 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T06:57:02 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.3?vdb-ctx=refseq'... 2020-06-21T06:57:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T06:57:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T06:57:15 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T06:57:15 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.4?vdb-ctx=refseq'... 2020-06-21T06:57:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T06:57:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T06:57:37 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T06:57:37 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.2?vdb-ctx=refseq'... 2020-06-21T06:57:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T06:57:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T06:57:58 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T06:57:58 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.4?vdb-ctx=refseq'... 2020-06-21T06:57:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T06:58:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T06:58:17 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T06:58:17 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CM000457.1?vdb-ctx=refseq'... 2020-06-21T06:58:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T06:58:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T06:58:31 prefetch.2.10.7: 8) 'ncbi-acc:CM000457.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T06:58:31 prefetch.2.10.7: 9) Downloading 'ncbi-acc:CM000458.1?vdb-ctx=refseq'... 2020-06-21T06:58:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T06:58:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T06:58:46 prefetch.2.10.7: 9) 'ncbi-acc:CM000458.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T06:58:46 prefetch.2.10.7: 10) Downloading 'ncbi-acc:CM000459.1?vdb-ctx=refseq'... 2020-06-21T06:58:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T06:58:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T06:58:59 prefetch.2.10.7: 10) 'ncbi-acc:CM000459.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T06:58:59 prefetch.2.10.7: 11) Downloading 'ncbi-acc:FA000001.1?vdb-ctx=refseq'... 2020-06-21T06:58:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T06:59:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T06:59:14 prefetch.2.10.7: 11) 'ncbi-acc:FA000001.1?vdb-ctx=refseq' was downloaded successfully Read 24435944 spots for ERR031133/ERR031133.sra Written 24435944 spots for ERR031133/ERR031133.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: 00:03:19 24435944 reads; of these: 24435944 (100.00%) were unpaired; of these: 757793 (3.10%) aligned 0 times 20811273 (85.17%) aligned exactly 1 time 2866878 (11.73%) aligned >1 times 96.90% overall alignment rate Time searching: 00:03:19 Overall time: 00:03:19 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 9542141 / 23678151 = 0.4030 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 @ Sun, 21 Jun 2020 16:07:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 16:07:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:07:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:07:37: 1000000 INFO @ Sun, 21 Jun 2020 16:07:42: 2000000 INFO @ Sun, 21 Jun 2020 16:07:47: 3000000 INFO @ Sun, 21 Jun 2020 16:07:52: 4000000 INFO @ Sun, 21 Jun 2020 16:07:57: 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 @ Sun, 21 Jun 2020 16:08:02: 6000000 INFO @ Sun, 21 Jun 2020 16:08:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 16:08:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:08:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:08:07: 7000000 INFO @ Sun, 21 Jun 2020 16:08:08: 1000000 INFO @ Sun, 21 Jun 2020 16:08:13: 8000000 INFO @ Sun, 21 Jun 2020 16:08:15: 2000000 INFO @ Sun, 21 Jun 2020 16:08:18: 9000000 INFO @ Sun, 21 Jun 2020 16:08:21: 3000000 INFO @ Sun, 21 Jun 2020 16:08:24: 10000000 INFO @ Sun, 21 Jun 2020 16:08:27: 4000000 INFO @ Sun, 21 Jun 2020 16:08:30: 11000000 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 @ Sun, 21 Jun 2020 16:08:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 16:08:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:08:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:08:33: 5000000 INFO @ Sun, 21 Jun 2020 16:08:36: 12000000 INFO @ Sun, 21 Jun 2020 16:08:38: 1000000 INFO @ Sun, 21 Jun 2020 16:08:40: 6000000 INFO @ Sun, 21 Jun 2020 16:08:41: 13000000 INFO @ Sun, 21 Jun 2020 16:08:44: 2000000 INFO @ Sun, 21 Jun 2020 16:08:46: 7000000 INFO @ Sun, 21 Jun 2020 16:08:47: 14000000 INFO @ Sun, 21 Jun 2020 16:08:48: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:08:48: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:08:48: #1 total tags in treatment: 14136010 INFO @ Sun, 21 Jun 2020 16:08:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:08:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 16:08:49: #1 tags after filtering in treatment: 14136004 INFO @ Sun, 21 Jun 2020 16:08:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:08:49: #1 finished! INFO @ Sun, 21 Jun 2020 16:08:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:08:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:08:49: 3000000 INFO @ Sun, 21 Jun 2020 16:08:50: #2 number of paired peaks: 1776 INFO @ Sun, 21 Jun 2020 16:08:50: start model_add_line... INFO @ Sun, 21 Jun 2020 16:08:50: start X-correlation... INFO @ Sun, 21 Jun 2020 16:08:50: end of X-cor INFO @ Sun, 21 Jun 2020 16:08:50: #2 finished! INFO @ Sun, 21 Jun 2020 16:08:50: #2 predicted fragment length is 172 bps INFO @ Sun, 21 Jun 2020 16:08:50: #2 alternative fragment length(s) may be 172 bps INFO @ Sun, 21 Jun 2020 16:08:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.05_model.r INFO @ Sun, 21 Jun 2020 16:08:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:08:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:08:52: 8000000 INFO @ Sun, 21 Jun 2020 16:08:55: 4000000 INFO @ Sun, 21 Jun 2020 16:08:59: 9000000 INFO @ Sun, 21 Jun 2020 16:09:01: 5000000 INFO @ Sun, 21 Jun 2020 16:09:05: 10000000 INFO @ Sun, 21 Jun 2020 16:09:06: 6000000 INFO @ Sun, 21 Jun 2020 16:09:11: 11000000 INFO @ Sun, 21 Jun 2020 16:09:12: 7000000 INFO @ Sun, 21 Jun 2020 16:09:18: 8000000 INFO @ Sun, 21 Jun 2020 16:09:18: 12000000 INFO @ Sun, 21 Jun 2020 16:09:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:09:23: 9000000 INFO @ Sun, 21 Jun 2020 16:09:24: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:09:29: 10000000 INFO @ Sun, 21 Jun 2020 16:09:31: 14000000 INFO @ Sun, 21 Jun 2020 16:09:32: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:09:32: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:09:32: #1 total tags in treatment: 14136010 INFO @ Sun, 21 Jun 2020 16:09:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:09:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 16:09:32: #1 tags after filtering in treatment: 14136004 INFO @ Sun, 21 Jun 2020 16:09:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:09:32: #1 finished! INFO @ Sun, 21 Jun 2020 16:09:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:09:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:09:33: #2 number of paired peaks: 1776 INFO @ Sun, 21 Jun 2020 16:09:33: start model_add_line... INFO @ Sun, 21 Jun 2020 16:09:33: start X-correlation... INFO @ Sun, 21 Jun 2020 16:09:33: end of X-cor INFO @ Sun, 21 Jun 2020 16:09:33: #2 finished! INFO @ Sun, 21 Jun 2020 16:09:33: #2 predicted fragment length is 172 bps INFO @ Sun, 21 Jun 2020 16:09:33: #2 alternative fragment length(s) may be 172 bps INFO @ Sun, 21 Jun 2020 16:09:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.10_model.r INFO @ Sun, 21 Jun 2020 16:09:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:09:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:09:35: 11000000 INFO @ Sun, 21 Jun 2020 16:09:40: 12000000 INFO @ Sun, 21 Jun 2020 16:09:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:09:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:09:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.05_summits.bed INFO @ Sun, 21 Jun 2020 16:09:41: Done! pass1 - making usageList (235 chroms): 2 millis pass2 - checking and writing primary data (11269 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:09:45: 13000000 INFO @ Sun, 21 Jun 2020 16:09:51: 14000000 INFO @ Sun, 21 Jun 2020 16:09:51: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:09:51: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:09:51: #1 total tags in treatment: 14136010 INFO @ Sun, 21 Jun 2020 16:09:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:09:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 16:09:52: #1 tags after filtering in treatment: 14136004 INFO @ Sun, 21 Jun 2020 16:09:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:09:52: #1 finished! INFO @ Sun, 21 Jun 2020 16:09:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:09:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:09:53: #2 number of paired peaks: 1776 INFO @ Sun, 21 Jun 2020 16:09:53: start model_add_line... INFO @ Sun, 21 Jun 2020 16:09:53: start X-correlation... INFO @ Sun, 21 Jun 2020 16:09:53: end of X-cor INFO @ Sun, 21 Jun 2020 16:09:53: #2 finished! INFO @ Sun, 21 Jun 2020 16:09:53: #2 predicted fragment length is 172 bps INFO @ Sun, 21 Jun 2020 16:09:53: #2 alternative fragment length(s) may be 172 bps INFO @ Sun, 21 Jun 2020 16:09:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.20_model.r INFO @ Sun, 21 Jun 2020 16:09:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:09:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:10:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:10:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:10:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:10:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.10_summits.bed INFO @ Sun, 21 Jun 2020 16:10:25: Done! pass1 - making usageList (185 chroms): 2 millis pass2 - checking and writing primary data (6126 records, 4 fields): 57 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:10:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:10:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:10:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:10:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011412/ERX011412.20_summits.bed INFO @ Sun, 21 Jun 2020 16:10:44: Done! pass1 - making usageList (108 chroms): 1 millis pass2 - checking and writing primary data (1881 records, 4 fields): 8 millis CompletedMACS2peakCalling