Job ID = 6451794 SRX = ERX011413 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:28:05 prefetch.2.10.7: 1) Downloading 'ERR031134'... 2020-06-21T07:28:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:30:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:30:30 prefetch.2.10.7: 'ERR031134' is valid 2020-06-21T07:30:30 prefetch.2.10.7: 1) 'ERR031134' was downloaded successfully 2020-06-21T07:31:22 prefetch.2.10.7: 'ERR031134' has 10 unresolved dependencies 2020-06-21T07:31:22 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.4?vdb-ctx=refseq'... 2020-06-21T07:31:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:32:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:32:07 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:32:07 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.5?vdb-ctx=refseq'... 2020-06-21T07:32:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:32:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:32:24 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:32:24 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.3?vdb-ctx=refseq'... 2020-06-21T07:32:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:32:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:32:35 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:32:35 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.4?vdb-ctx=refseq'... 2020-06-21T07:32:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:32:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:32:52 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:32:52 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.2?vdb-ctx=refseq'... 2020-06-21T07:32:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:33:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:33:08 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:33:08 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.4?vdb-ctx=refseq'... 2020-06-21T07:33:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:33:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:33:26 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:33:26 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CM000457.1?vdb-ctx=refseq'... 2020-06-21T07:33:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:33:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:33:39 prefetch.2.10.7: 8) 'ncbi-acc:CM000457.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:33:39 prefetch.2.10.7: 9) Downloading 'ncbi-acc:CM000458.1?vdb-ctx=refseq'... 2020-06-21T07:33:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:33:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:33:53 prefetch.2.10.7: 9) 'ncbi-acc:CM000458.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:33:53 prefetch.2.10.7: 10) Downloading 'ncbi-acc:CM000459.1?vdb-ctx=refseq'... 2020-06-21T07:33:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:34:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:34:06 prefetch.2.10.7: 10) 'ncbi-acc:CM000459.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:34:06 prefetch.2.10.7: 11) Downloading 'ncbi-acc:FA000001.1?vdb-ctx=refseq'... 2020-06-21T07:34:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:34:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:34:22 prefetch.2.10.7: 11) 'ncbi-acc:FA000001.1?vdb-ctx=refseq' was downloaded successfully Read 24722284 spots for ERR031134/ERR031134.sra Written 24722284 spots for ERR031134/ERR031134.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: 00:04:41 24722284 reads; of these: 24722284 (100.00%) were unpaired; of these: 1054737 (4.27%) aligned 0 times 18248330 (73.81%) aligned exactly 1 time 5419217 (21.92%) aligned >1 times 95.73% overall alignment rate Time searching: 00:04:41 Overall time: 00:04:41 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] 14221849 / 23667547 = 0.6009 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 16:44:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.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 16:44:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:44:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:44:19: 1000000 INFO @ Sun, 21 Jun 2020 16:44:23: 2000000 INFO @ Sun, 21 Jun 2020 16:44:28: 3000000 INFO @ Sun, 21 Jun 2020 16:44:32: 4000000 INFO @ Sun, 21 Jun 2020 16:44:37: 5000000 INFO @ Sun, 21 Jun 2020 16:44:42: 6000000 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 16:44:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.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 16:44:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:44:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:44:47: 7000000 INFO @ Sun, 21 Jun 2020 16:44:49: 1000000 INFO @ Sun, 21 Jun 2020 16:44:52: 8000000 INFO @ Sun, 21 Jun 2020 16:44:54: 2000000 INFO @ Sun, 21 Jun 2020 16:44:57: 9000000 INFO @ Sun, 21 Jun 2020 16:44:59: 3000000 INFO @ Sun, 21 Jun 2020 16:44:59: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:44:59: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:44:59: #1 total tags in treatment: 9445698 INFO @ Sun, 21 Jun 2020 16:44:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:44:59: #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 16:45:00: #1 tags after filtering in treatment: 9445695 INFO @ Sun, 21 Jun 2020 16:45:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:45:00: #1 finished! INFO @ Sun, 21 Jun 2020 16:45:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:45:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:45:01: #2 number of paired peaks: 3201 INFO @ Sun, 21 Jun 2020 16:45:01: start model_add_line... INFO @ Sun, 21 Jun 2020 16:45:01: start X-correlation... INFO @ Sun, 21 Jun 2020 16:45:01: end of X-cor INFO @ Sun, 21 Jun 2020 16:45:01: #2 finished! INFO @ Sun, 21 Jun 2020 16:45:01: #2 predicted fragment length is 193 bps INFO @ Sun, 21 Jun 2020 16:45:01: #2 alternative fragment length(s) may be 193 bps INFO @ Sun, 21 Jun 2020 16:45:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.05_model.r INFO @ Sun, 21 Jun 2020 16:45:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:45:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:45:04: 4000000 INFO @ Sun, 21 Jun 2020 16:45:09: 5000000 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 16:45:13: 6000000 INFO @ Sun, 21 Jun 2020 16:45:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.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 16:45:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:45:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:45:18: 7000000 INFO @ Sun, 21 Jun 2020 16:45:20: 1000000 INFO @ Sun, 21 Jun 2020 16:45:24: 8000000 INFO @ Sun, 21 Jun 2020 16:45:25: 2000000 INFO @ Sun, 21 Jun 2020 16:45:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:45:29: 9000000 INFO @ Sun, 21 Jun 2020 16:45:30: 3000000 INFO @ Sun, 21 Jun 2020 16:45:31: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:45:31: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:45:31: #1 total tags in treatment: 9445698 INFO @ Sun, 21 Jun 2020 16:45:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:45:31: #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 16:45:32: #1 tags after filtering in treatment: 9445695 INFO @ Sun, 21 Jun 2020 16:45:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:45:32: #1 finished! INFO @ Sun, 21 Jun 2020 16:45:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:45:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:45:33: #2 number of paired peaks: 3201 INFO @ Sun, 21 Jun 2020 16:45:33: start model_add_line... INFO @ Sun, 21 Jun 2020 16:45:33: start X-correlation... INFO @ Sun, 21 Jun 2020 16:45:33: end of X-cor INFO @ Sun, 21 Jun 2020 16:45:33: #2 finished! INFO @ Sun, 21 Jun 2020 16:45:33: #2 predicted fragment length is 193 bps INFO @ Sun, 21 Jun 2020 16:45:33: #2 alternative fragment length(s) may be 193 bps INFO @ Sun, 21 Jun 2020 16:45:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.10_model.r INFO @ Sun, 21 Jun 2020 16:45:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:45:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:45:35: 4000000 INFO @ Sun, 21 Jun 2020 16:45:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:45:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:45:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.05_summits.bed INFO @ Sun, 21 Jun 2020 16:45:38: Done! pass1 - making usageList (813 chroms): 2 millis pass2 - checking and writing primary data (6889 records, 4 fields): 170 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:45:39: 5000000 INFO @ Sun, 21 Jun 2020 16:45:44: 6000000 INFO @ Sun, 21 Jun 2020 16:45:49: 7000000 INFO @ Sun, 21 Jun 2020 16:45:54: 8000000 INFO @ Sun, 21 Jun 2020 16:45:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:45:59: 9000000 INFO @ Sun, 21 Jun 2020 16:46:02: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:46:02: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:46:02: #1 total tags in treatment: 9445698 INFO @ Sun, 21 Jun 2020 16:46:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:46:02: #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 16:46:02: #1 tags after filtering in treatment: 9445695 INFO @ Sun, 21 Jun 2020 16:46:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:46:02: #1 finished! INFO @ Sun, 21 Jun 2020 16:46:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:46:02: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:46:03: #2 number of paired peaks: 3201 INFO @ Sun, 21 Jun 2020 16:46:03: start model_add_line... INFO @ Sun, 21 Jun 2020 16:46:03: start X-correlation... INFO @ Sun, 21 Jun 2020 16:46:03: end of X-cor INFO @ Sun, 21 Jun 2020 16:46:03: #2 finished! INFO @ Sun, 21 Jun 2020 16:46:03: #2 predicted fragment length is 193 bps INFO @ Sun, 21 Jun 2020 16:46:03: #2 alternative fragment length(s) may be 193 bps INFO @ Sun, 21 Jun 2020 16:46:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.20_model.r INFO @ Sun, 21 Jun 2020 16:46:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:46:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:46:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:46:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:46:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.10_summits.bed INFO @ Sun, 21 Jun 2020 16:46:10: Done! pass1 - making usageList (695 chroms): 1 millis pass2 - checking and writing primary data (5503 records, 4 fields): 25 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:46:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:46:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:46:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:46:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011413/ERX011413.20_summits.bed INFO @ Sun, 21 Jun 2020 16:46:40: Done! pass1 - making usageList (567 chroms): 2 millis pass2 - checking and writing primary data (4334 records, 4 fields): 21 millis CompletedMACS2peakCalling