Job ID = 6451787 SRX = ERX011409 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T06:57:43 prefetch.2.10.7: 1) Downloading 'ERR031130'... 2020-06-21T06:57:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:02:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:02:56 prefetch.2.10.7: 'ERR031130' is valid 2020-06-21T07:02:56 prefetch.2.10.7: 1) 'ERR031130' was downloaded successfully 2020-06-21T07:03:47 prefetch.2.10.7: 'ERR031130' has 10 unresolved dependencies 2020-06-21T07:03:47 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.4?vdb-ctx=refseq'... 2020-06-21T07:03:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:04:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:04:04 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:04:04 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.5?vdb-ctx=refseq'... 2020-06-21T07:04:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:04:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:04:19 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:04:19 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.3?vdb-ctx=refseq'... 2020-06-21T07:04:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:04:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:04:31 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:04:31 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.4?vdb-ctx=refseq'... 2020-06-21T07:04:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:04:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:04:49 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:04:49 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.2?vdb-ctx=refseq'... 2020-06-21T07:04:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:05:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:05:10 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:05:10 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.4?vdb-ctx=refseq'... 2020-06-21T07:05:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:05:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:05:27 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:05:27 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CM000457.1?vdb-ctx=refseq'... 2020-06-21T07:05:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:05:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:05:40 prefetch.2.10.7: 8) 'ncbi-acc:CM000457.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:05:40 prefetch.2.10.7: 9) Downloading 'ncbi-acc:CM000458.1?vdb-ctx=refseq'... 2020-06-21T07:05:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:05:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:05:54 prefetch.2.10.7: 9) 'ncbi-acc:CM000458.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:05:54 prefetch.2.10.7: 10) Downloading 'ncbi-acc:CM000459.1?vdb-ctx=refseq'... 2020-06-21T07:05:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:06:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:06:07 prefetch.2.10.7: 10) 'ncbi-acc:CM000459.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:06:07 prefetch.2.10.7: 11) Downloading 'ncbi-acc:FA000001.1?vdb-ctx=refseq'... 2020-06-21T07:06:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:06:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:06:21 prefetch.2.10.7: 11) 'ncbi-acc:FA000001.1?vdb-ctx=refseq' was downloaded successfully Read 25880232 spots for ERR031130/ERR031130.sra Written 25880232 spots for ERR031130/ERR031130.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: 00:04:17 25880232 reads; of these: 25880232 (100.00%) were unpaired; of these: 806595 (3.12%) aligned 0 times 21391001 (82.65%) aligned exactly 1 time 3682636 (14.23%) aligned >1 times 96.88% overall alignment rate Time searching: 00:04:17 Overall time: 00:04:17 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] 7346269 / 25073637 = 0.2930 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 16:16:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.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 16:16:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:16:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:16:34: 1000000 INFO @ Sun, 21 Jun 2020 16:16:41: 2000000 INFO @ Sun, 21 Jun 2020 16:16:47: 3000000 INFO @ Sun, 21 Jun 2020 16:16:53: 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 @ Sun, 21 Jun 2020 16:16:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.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 16:16:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:16:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:17:00: 5000000 INFO @ Sun, 21 Jun 2020 16:17:06: 1000000 INFO @ Sun, 21 Jun 2020 16:17:07: 6000000 INFO @ Sun, 21 Jun 2020 16:17:13: 2000000 INFO @ Sun, 21 Jun 2020 16:17:14: 7000000 INFO @ Sun, 21 Jun 2020 16:17:19: 3000000 INFO @ Sun, 21 Jun 2020 16:17:21: 8000000 INFO @ Sun, 21 Jun 2020 16:17:26: 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 @ Sun, 21 Jun 2020 16:17:28: 9000000 INFO @ Sun, 21 Jun 2020 16:17:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.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 16:17:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:17:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:17:33: 5000000 INFO @ Sun, 21 Jun 2020 16:17:35: 10000000 INFO @ Sun, 21 Jun 2020 16:17:36: 1000000 INFO @ Sun, 21 Jun 2020 16:17:41: 6000000 INFO @ Sun, 21 Jun 2020 16:17:42: 11000000 INFO @ Sun, 21 Jun 2020 16:17:43: 2000000 INFO @ Sun, 21 Jun 2020 16:17:48: 7000000 INFO @ Sun, 21 Jun 2020 16:17:50: 12000000 INFO @ Sun, 21 Jun 2020 16:17:50: 3000000 INFO @ Sun, 21 Jun 2020 16:17:55: 8000000 INFO @ Sun, 21 Jun 2020 16:17:57: 13000000 INFO @ Sun, 21 Jun 2020 16:17:58: 4000000 INFO @ Sun, 21 Jun 2020 16:18:02: 9000000 INFO @ Sun, 21 Jun 2020 16:18:04: 14000000 INFO @ Sun, 21 Jun 2020 16:18:06: 5000000 INFO @ Sun, 21 Jun 2020 16:18:09: 10000000 INFO @ Sun, 21 Jun 2020 16:18:11: 15000000 INFO @ Sun, 21 Jun 2020 16:18:13: 6000000 INFO @ Sun, 21 Jun 2020 16:18:16: 11000000 INFO @ Sun, 21 Jun 2020 16:18:18: 16000000 INFO @ Sun, 21 Jun 2020 16:18:20: 7000000 INFO @ Sun, 21 Jun 2020 16:18:23: 12000000 INFO @ Sun, 21 Jun 2020 16:18:25: 17000000 INFO @ Sun, 21 Jun 2020 16:18:27: 8000000 INFO @ Sun, 21 Jun 2020 16:18:30: 13000000 INFO @ Sun, 21 Jun 2020 16:18:31: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:18:31: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:18:31: #1 total tags in treatment: 17727368 INFO @ Sun, 21 Jun 2020 16:18:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:18:31: #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 16:18:31: #1 tags after filtering in treatment: 17727361 INFO @ Sun, 21 Jun 2020 16:18:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:18:31: #1 finished! INFO @ Sun, 21 Jun 2020 16:18:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:18:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:18:33: #2 number of paired peaks: 1154 INFO @ Sun, 21 Jun 2020 16:18:33: start model_add_line... INFO @ Sun, 21 Jun 2020 16:18:33: start X-correlation... INFO @ Sun, 21 Jun 2020 16:18:33: end of X-cor INFO @ Sun, 21 Jun 2020 16:18:33: #2 finished! INFO @ Sun, 21 Jun 2020 16:18:33: #2 predicted fragment length is 187 bps INFO @ Sun, 21 Jun 2020 16:18:33: #2 alternative fragment length(s) may be 187 bps INFO @ Sun, 21 Jun 2020 16:18:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.05_model.r INFO @ Sun, 21 Jun 2020 16:18:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:18:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:18:35: 9000000 INFO @ Sun, 21 Jun 2020 16:18:38: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:18:42: 10000000 INFO @ Sun, 21 Jun 2020 16:18:45: 15000000 INFO @ Sun, 21 Jun 2020 16:18:49: 11000000 INFO @ Sun, 21 Jun 2020 16:18:52: 16000000 INFO @ Sun, 21 Jun 2020 16:18:56: 12000000 INFO @ Sun, 21 Jun 2020 16:18:59: 17000000 INFO @ Sun, 21 Jun 2020 16:19:03: 13000000 INFO @ Sun, 21 Jun 2020 16:19:05: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:19:05: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:19:05: #1 total tags in treatment: 17727368 INFO @ Sun, 21 Jun 2020 16:19:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:19:05: #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 16:19:05: #1 tags after filtering in treatment: 17727361 INFO @ Sun, 21 Jun 2020 16:19:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:19:05: #1 finished! INFO @ Sun, 21 Jun 2020 16:19:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:19:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:19:06: #2 number of paired peaks: 1154 INFO @ Sun, 21 Jun 2020 16:19:06: start model_add_line... INFO @ Sun, 21 Jun 2020 16:19:07: start X-correlation... INFO @ Sun, 21 Jun 2020 16:19:07: end of X-cor INFO @ Sun, 21 Jun 2020 16:19:07: #2 finished! INFO @ Sun, 21 Jun 2020 16:19:07: #2 predicted fragment length is 187 bps INFO @ Sun, 21 Jun 2020 16:19:07: #2 alternative fragment length(s) may be 187 bps INFO @ Sun, 21 Jun 2020 16:19:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.10_model.r INFO @ Sun, 21 Jun 2020 16:19:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:19:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:19:09: 14000000 INFO @ Sun, 21 Jun 2020 16:19:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:19:16: 15000000 INFO @ Sun, 21 Jun 2020 16:19:22: 16000000 INFO @ Sun, 21 Jun 2020 16:19:28: 17000000 INFO @ Sun, 21 Jun 2020 16:19:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:19:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:19:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.05_summits.bed INFO @ Sun, 21 Jun 2020 16:19:32: Done! pass1 - making usageList (247 chroms): 2 millis pass2 - checking and writing primary data (8392 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:19:33: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:19:33: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:19:33: #1 total tags in treatment: 17727368 INFO @ Sun, 21 Jun 2020 16:19:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:19:33: #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 16:19:34: #1 tags after filtering in treatment: 17727361 INFO @ Sun, 21 Jun 2020 16:19:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:19:34: #1 finished! INFO @ Sun, 21 Jun 2020 16:19:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:19:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:19:35: #2 number of paired peaks: 1154 INFO @ Sun, 21 Jun 2020 16:19:35: start model_add_line... INFO @ Sun, 21 Jun 2020 16:19:35: start X-correlation... INFO @ Sun, 21 Jun 2020 16:19:35: end of X-cor INFO @ Sun, 21 Jun 2020 16:19:35: #2 finished! INFO @ Sun, 21 Jun 2020 16:19:35: #2 predicted fragment length is 187 bps INFO @ Sun, 21 Jun 2020 16:19:35: #2 alternative fragment length(s) may be 187 bps INFO @ Sun, 21 Jun 2020 16:19:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.20_model.r INFO @ Sun, 21 Jun 2020 16:19:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:19:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:19:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:20:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:20:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:20:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.10_summits.bed INFO @ Sun, 21 Jun 2020 16:20:08: Done! pass1 - making usageList (208 chroms): 2 millis pass2 - checking and writing primary data (6322 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:20:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:20:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:20:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:20:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011409/ERX011409.20_summits.bed INFO @ Sun, 21 Jun 2020 16:20:36: Done! pass1 - making usageList (145 chroms): 1 millis pass2 - checking and writing primary data (4055 records, 4 fields): 9 millis CompletedMACS2peakCalling