Job ID = 6459815 SRX = SRX859013 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:33:13 prefetch.2.10.7: 1) Downloading 'SRR1779569'... 2020-06-21T13:33:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:34:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:34:09 prefetch.2.10.7: 'SRR1779569' is valid 2020-06-21T13:34:09 prefetch.2.10.7: 1) 'SRR1779569' was downloaded successfully 2020-06-21T13:35:01 prefetch.2.10.7: 'SRR1779569' has 10 unresolved dependencies 2020-06-21T13:35:01 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.4?vdb-ctx=refseq'... 2020-06-21T13:35:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:35:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:35:17 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:35:17 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.5?vdb-ctx=refseq'... 2020-06-21T13:35:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:35:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:35:39 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:35:39 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.3?vdb-ctx=refseq'... 2020-06-21T13:35:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:35:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:35:50 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:35:50 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.4?vdb-ctx=refseq'... 2020-06-21T13:35:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:36:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:36:08 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:36:08 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.2?vdb-ctx=refseq'... 2020-06-21T13:36:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:36:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:36:27 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:36:27 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.4?vdb-ctx=refseq'... 2020-06-21T13:36:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:36:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:36:46 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:36:46 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CM000457.1?vdb-ctx=refseq'... 2020-06-21T13:36:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:37:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:37:00 prefetch.2.10.7: 8) 'ncbi-acc:CM000457.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:37:00 prefetch.2.10.7: 9) Downloading 'ncbi-acc:CM000458.1?vdb-ctx=refseq'... 2020-06-21T13:37:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:37:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:37:13 prefetch.2.10.7: 9) 'ncbi-acc:CM000458.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:37:13 prefetch.2.10.7: 10) Downloading 'ncbi-acc:CM000459.1?vdb-ctx=refseq'... 2020-06-21T13:37:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:37:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:37:27 prefetch.2.10.7: 10) 'ncbi-acc:CM000459.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:37:27 prefetch.2.10.7: 11) Downloading 'ncbi-acc:FA000001.1?vdb-ctx=refseq'... 2020-06-21T13:37:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:37:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:37:42 prefetch.2.10.7: 11) 'ncbi-acc:FA000001.1?vdb-ctx=refseq' was downloaded successfully Read 10963496 spots for SRR1779569/SRR1779569.sra Written 10963496 spots for SRR1779569/SRR1779569.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: 00:01:53 10963496 reads; of these: 10963496 (100.00%) were unpaired; of these: 59950 (0.55%) aligned 0 times 10480086 (95.59%) aligned exactly 1 time 423460 (3.86%) aligned >1 times 99.45% overall alignment rate Time searching: 00:01:53 Overall time: 00:01:53 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] 3931 / 10903546 = 0.0004 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 22:43:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.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 22:43:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:43:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:43:33: 1000000 INFO @ Sun, 21 Jun 2020 22:43:38: 2000000 INFO @ Sun, 21 Jun 2020 22:43:43: 3000000 INFO @ Sun, 21 Jun 2020 22:43:48: 4000000 INFO @ Sun, 21 Jun 2020 22:43:53: 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 22:43:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.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 22:43:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:43:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:43:58: 6000000 INFO @ Sun, 21 Jun 2020 22:44:03: 1000000 INFO @ Sun, 21 Jun 2020 22:44:04: 7000000 INFO @ Sun, 21 Jun 2020 22:44:09: 2000000 INFO @ Sun, 21 Jun 2020 22:44:09: 8000000 INFO @ Sun, 21 Jun 2020 22:44:14: 3000000 INFO @ Sun, 21 Jun 2020 22:44:14: 9000000 INFO @ Sun, 21 Jun 2020 22:44:20: 4000000 INFO @ Sun, 21 Jun 2020 22:44:20: 10000000 INFO @ Sun, 21 Jun 2020 22:44:25: 5000000 INFO @ Sun, 21 Jun 2020 22:44:25: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:44:25: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:44:25: #1 total tags in treatment: 10899615 INFO @ Sun, 21 Jun 2020 22:44:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:44:25: #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 22:44:25: #1 tags after filtering in treatment: 10899333 INFO @ Sun, 21 Jun 2020 22:44:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:44:25: #1 finished! INFO @ Sun, 21 Jun 2020 22:44:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:44:25: #2 looking for paired plus/minus strand peaks... 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 22:44:26: #2 number of paired peaks: 2001 INFO @ Sun, 21 Jun 2020 22:44:26: start model_add_line... INFO @ Sun, 21 Jun 2020 22:44:26: start X-correlation... INFO @ Sun, 21 Jun 2020 22:44:26: end of X-cor INFO @ Sun, 21 Jun 2020 22:44:26: #2 finished! INFO @ Sun, 21 Jun 2020 22:44:26: #2 predicted fragment length is 151 bps INFO @ Sun, 21 Jun 2020 22:44:26: #2 alternative fragment length(s) may be 151 bps INFO @ Sun, 21 Jun 2020 22:44:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.05_model.r INFO @ Sun, 21 Jun 2020 22:44:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:44:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:44:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.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 22:44:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:44:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:44:31: 6000000 INFO @ Sun, 21 Jun 2020 22:44:34: 1000000 INFO @ Sun, 21 Jun 2020 22:44:37: 7000000 INFO @ Sun, 21 Jun 2020 22:44:40: 2000000 INFO @ Sun, 21 Jun 2020 22:44:42: 8000000 INFO @ Sun, 21 Jun 2020 22:44:47: 3000000 INFO @ Sun, 21 Jun 2020 22:44:48: 9000000 INFO @ Sun, 21 Jun 2020 22:44:53: 4000000 INFO @ Sun, 21 Jun 2020 22:44:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:44:54: 10000000 INFO @ Sun, 21 Jun 2020 22:44:59: 5000000 INFO @ Sun, 21 Jun 2020 22:44:59: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:44:59: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:44:59: #1 total tags in treatment: 10899615 INFO @ Sun, 21 Jun 2020 22:44:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:44:59: #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 22:45:00: #1 tags after filtering in treatment: 10899333 INFO @ Sun, 21 Jun 2020 22:45:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:45:00: #1 finished! INFO @ Sun, 21 Jun 2020 22:45:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:45:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:45:00: #2 number of paired peaks: 2001 INFO @ Sun, 21 Jun 2020 22:45:00: start model_add_line... INFO @ Sun, 21 Jun 2020 22:45:00: start X-correlation... INFO @ Sun, 21 Jun 2020 22:45:01: end of X-cor INFO @ Sun, 21 Jun 2020 22:45:01: #2 finished! INFO @ Sun, 21 Jun 2020 22:45:01: #2 predicted fragment length is 151 bps INFO @ Sun, 21 Jun 2020 22:45:01: #2 alternative fragment length(s) may be 151 bps INFO @ Sun, 21 Jun 2020 22:45:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.10_model.r INFO @ Sun, 21 Jun 2020 22:45:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:45:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:45:05: 6000000 INFO @ Sun, 21 Jun 2020 22:45:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:45:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:45:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.05_summits.bed INFO @ Sun, 21 Jun 2020 22:45:07: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (5169 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:45:11: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:45:17: 8000000 INFO @ Sun, 21 Jun 2020 22:45:23: 9000000 INFO @ Sun, 21 Jun 2020 22:45:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:45:29: 10000000 INFO @ Sun, 21 Jun 2020 22:45:34: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:45:34: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:45:34: #1 total tags in treatment: 10899615 INFO @ Sun, 21 Jun 2020 22:45:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:45:34: #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 22:45:35: #1 tags after filtering in treatment: 10899333 INFO @ Sun, 21 Jun 2020 22:45:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:45:35: #1 finished! INFO @ Sun, 21 Jun 2020 22:45:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:45:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:45:35: #2 number of paired peaks: 2001 INFO @ Sun, 21 Jun 2020 22:45:35: start model_add_line... INFO @ Sun, 21 Jun 2020 22:45:36: start X-correlation... INFO @ Sun, 21 Jun 2020 22:45:36: end of X-cor INFO @ Sun, 21 Jun 2020 22:45:36: #2 finished! INFO @ Sun, 21 Jun 2020 22:45:36: #2 predicted fragment length is 151 bps INFO @ Sun, 21 Jun 2020 22:45:36: #2 alternative fragment length(s) may be 151 bps INFO @ Sun, 21 Jun 2020 22:45:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.20_model.r INFO @ Sun, 21 Jun 2020 22:45:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:45:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:45:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:45:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:45:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.10_summits.bed INFO @ Sun, 21 Jun 2020 22:45:39: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (3447 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:46:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:46:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:46:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:46:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX859013/SRX859013.20_summits.bed INFO @ Sun, 21 Jun 2020 22:46:16: Done! pass1 - making usageList (22 chroms): 1 millis pass2 - checking and writing primary data (2079 records, 4 fields): 4 millis CompletedMACS2peakCalling