Job ID = 6508320 SRX = SRX2068662 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:01:11 prefetch.2.10.7: 1) Downloading 'SRR4101018'... 2020-06-26T14:01:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:04:21 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:04:21 prefetch.2.10.7: 1) 'SRR4101018' was downloaded successfully 2020-06-26T14:05:13 prefetch.2.10.7: 'SRR4101018' has 10 unresolved dependencies 2020-06-26T14:05:13 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.4?vdb-ctx=refseq'... 2020-06-26T14:05:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:05:30 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:05:30 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:05:30 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.5?vdb-ctx=refseq'... 2020-06-26T14:05:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:05:47 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:05:47 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.5?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:05:47 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.3?vdb-ctx=refseq'... 2020-06-26T14:05:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:06:00 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:06:00 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.3?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:06:00 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.4?vdb-ctx=refseq'... 2020-06-26T14:06:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:06:16 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:06:16 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:06:16 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.2?vdb-ctx=refseq'... 2020-06-26T14:06:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:06:36 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:06:36 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.2?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:06:36 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.4?vdb-ctx=refseq'... 2020-06-26T14:06:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:06:53 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:06:53 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:06:53 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CM000457.1?vdb-ctx=refseq'... 2020-06-26T14:06:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:07:07 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:07:07 prefetch.2.10.7: 8) 'ncbi-acc:CM000457.1?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:07:07 prefetch.2.10.7: 9) Downloading 'ncbi-acc:CM000458.1?vdb-ctx=refseq'... 2020-06-26T14:07:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:07:20 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:07:20 prefetch.2.10.7: 9) 'ncbi-acc:CM000458.1?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:07:20 prefetch.2.10.7: 10) Downloading 'ncbi-acc:CM000459.1?vdb-ctx=refseq'... 2020-06-26T14:07:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:07:34 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:07:34 prefetch.2.10.7: 10) 'ncbi-acc:CM000459.1?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:07:34 prefetch.2.10.7: 11) Downloading 'ncbi-acc:FA000001.1?vdb-ctx=refseq'... 2020-06-26T14:07:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:07:51 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:07:51 prefetch.2.10.7: 11) 'ncbi-acc:FA000001.1?vdb-ctx=refseq' was downloaded successfully Read 47610776 spots for SRR4101018/SRR4101018.sra Written 47610776 spots for SRR4101018/SRR4101018.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:37 47610776 reads; of these: 47610776 (100.00%) were unpaired; of these: 14855176 (31.20%) aligned 0 times 25510072 (53.58%) aligned exactly 1 time 7245528 (15.22%) aligned >1 times 68.80% overall alignment rate Time searching: 00:06:38 Overall time: 00:06:38 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 16 files... [bam_rmdupse_core] 9703290 / 32755600 = 0.2962 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 23:24:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.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 @ Fri, 26 Jun 2020 23:24:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:24:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:25:01: 1000000 INFO @ Fri, 26 Jun 2020 23:25:07: 2000000 INFO @ Fri, 26 Jun 2020 23:25:12: 3000000 INFO @ Fri, 26 Jun 2020 23:25:17: 4000000 INFO @ Fri, 26 Jun 2020 23:25:23: 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 @ Fri, 26 Jun 2020 23:25:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.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 @ Fri, 26 Jun 2020 23:25:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:25:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:25:28: 6000000 INFO @ Fri, 26 Jun 2020 23:25:32: 1000000 INFO @ Fri, 26 Jun 2020 23:25:34: 7000000 INFO @ Fri, 26 Jun 2020 23:25:39: 2000000 INFO @ Fri, 26 Jun 2020 23:25:39: 8000000 INFO @ Fri, 26 Jun 2020 23:25:45: 9000000 INFO @ Fri, 26 Jun 2020 23:25:45: 3000000 INFO @ Fri, 26 Jun 2020 23:25:50: 10000000 INFO @ Fri, 26 Jun 2020 23:25:52: 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 @ Fri, 26 Jun 2020 23:25:56: 11000000 INFO @ Fri, 26 Jun 2020 23:25:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.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 @ Fri, 26 Jun 2020 23:25:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:25:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:25:58: 5000000 INFO @ Fri, 26 Jun 2020 23:26:02: 12000000 INFO @ Fri, 26 Jun 2020 23:26:02: 1000000 INFO @ Fri, 26 Jun 2020 23:26:04: 6000000 INFO @ Fri, 26 Jun 2020 23:26:08: 13000000 INFO @ Fri, 26 Jun 2020 23:26:09: 2000000 INFO @ Fri, 26 Jun 2020 23:26:11: 7000000 INFO @ Fri, 26 Jun 2020 23:26:13: 14000000 INFO @ Fri, 26 Jun 2020 23:26:15: 3000000 INFO @ Fri, 26 Jun 2020 23:26:17: 8000000 INFO @ Fri, 26 Jun 2020 23:26:19: 15000000 INFO @ Fri, 26 Jun 2020 23:26:22: 4000000 INFO @ Fri, 26 Jun 2020 23:26:24: 9000000 INFO @ Fri, 26 Jun 2020 23:26:25: 16000000 INFO @ Fri, 26 Jun 2020 23:26:28: 5000000 INFO @ Fri, 26 Jun 2020 23:26:30: 17000000 INFO @ Fri, 26 Jun 2020 23:26:30: 10000000 INFO @ Fri, 26 Jun 2020 23:26:34: 6000000 INFO @ Fri, 26 Jun 2020 23:26:36: 18000000 INFO @ Fri, 26 Jun 2020 23:26:37: 11000000 INFO @ Fri, 26 Jun 2020 23:26:41: 7000000 INFO @ Fri, 26 Jun 2020 23:26:42: 19000000 INFO @ Fri, 26 Jun 2020 23:26:43: 12000000 INFO @ Fri, 26 Jun 2020 23:26:47: 8000000 INFO @ Fri, 26 Jun 2020 23:26:48: 20000000 INFO @ Fri, 26 Jun 2020 23:26:50: 13000000 INFO @ Fri, 26 Jun 2020 23:26:53: 9000000 INFO @ Fri, 26 Jun 2020 23:26:53: 21000000 INFO @ Fri, 26 Jun 2020 23:26:57: 14000000 INFO @ Fri, 26 Jun 2020 23:26:59: 22000000 INFO @ Fri, 26 Jun 2020 23:27:00: 10000000 INFO @ Fri, 26 Jun 2020 23:27:03: 15000000 INFO @ Fri, 26 Jun 2020 23:27:04: 23000000 INFO @ Fri, 26 Jun 2020 23:27:05: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:27:05: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:27:05: #1 total tags in treatment: 23052310 INFO @ Fri, 26 Jun 2020 23:27:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:27:05: #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 23:27:06: #1 tags after filtering in treatment: 23052238 INFO @ Fri, 26 Jun 2020 23:27:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:27:06: #1 finished! INFO @ Fri, 26 Jun 2020 23:27:06: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:27:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:27:06: 11000000 INFO @ Fri, 26 Jun 2020 23:27:07: #2 number of paired peaks: 537 WARNING @ Fri, 26 Jun 2020 23:27:07: Fewer paired peaks (537) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 537 pairs to build model! INFO @ Fri, 26 Jun 2020 23:27:07: start model_add_line... INFO @ Fri, 26 Jun 2020 23:27:07: start X-correlation... INFO @ Fri, 26 Jun 2020 23:27:07: end of X-cor INFO @ Fri, 26 Jun 2020 23:27:07: #2 finished! INFO @ Fri, 26 Jun 2020 23:27:07: #2 predicted fragment length is 102 bps INFO @ Fri, 26 Jun 2020 23:27:07: #2 alternative fragment length(s) may be 102 bps INFO @ Fri, 26 Jun 2020 23:27:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.05_model.r INFO @ Fri, 26 Jun 2020 23:27:07: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:27:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:27:09: 16000000 INFO @ Fri, 26 Jun 2020 23:27:13: 12000000 INFO @ Fri, 26 Jun 2020 23:27:16: 17000000 INFO @ Fri, 26 Jun 2020 23:27:19: 13000000 INFO @ Fri, 26 Jun 2020 23:27:23: 18000000 INFO @ Fri, 26 Jun 2020 23:27:26: 14000000 INFO @ Fri, 26 Jun 2020 23:27:29: 19000000 INFO @ Fri, 26 Jun 2020 23:27:32: 15000000 INFO @ Fri, 26 Jun 2020 23:27:36: 20000000 INFO @ Fri, 26 Jun 2020 23:27:38: 16000000 INFO @ Fri, 26 Jun 2020 23:27:42: 21000000 INFO @ Fri, 26 Jun 2020 23:27:45: 17000000 INFO @ Fri, 26 Jun 2020 23:27:48: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:27:50: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:27:51: 18000000 INFO @ Fri, 26 Jun 2020 23:27:55: 23000000 INFO @ Fri, 26 Jun 2020 23:27:55: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:27:55: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:27:55: #1 total tags in treatment: 23052310 INFO @ Fri, 26 Jun 2020 23:27:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:27:55: #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 23:27:56: #1 tags after filtering in treatment: 23052238 INFO @ Fri, 26 Jun 2020 23:27:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:27:56: #1 finished! INFO @ Fri, 26 Jun 2020 23:27:56: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:27:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:27:57: #2 number of paired peaks: 537 WARNING @ Fri, 26 Jun 2020 23:27:57: Fewer paired peaks (537) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 537 pairs to build model! INFO @ Fri, 26 Jun 2020 23:27:57: start model_add_line... INFO @ Fri, 26 Jun 2020 23:27:58: start X-correlation... INFO @ Fri, 26 Jun 2020 23:27:58: end of X-cor INFO @ Fri, 26 Jun 2020 23:27:58: #2 finished! INFO @ Fri, 26 Jun 2020 23:27:58: #2 predicted fragment length is 102 bps INFO @ Fri, 26 Jun 2020 23:27:58: #2 alternative fragment length(s) may be 102 bps INFO @ Fri, 26 Jun 2020 23:27:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.10_model.r INFO @ Fri, 26 Jun 2020 23:27:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:27:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:27:58: 19000000 INFO @ Fri, 26 Jun 2020 23:28:04: 20000000 INFO @ Fri, 26 Jun 2020 23:28:10: 21000000 INFO @ Fri, 26 Jun 2020 23:28:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:28:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:28:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.05_summits.bed INFO @ Fri, 26 Jun 2020 23:28:11: Done! pass1 - making usageList (608 chroms): 2 millis pass2 - checking and writing primary data (3524 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:28:16: 22000000 INFO @ Fri, 26 Jun 2020 23:28:22: 23000000 INFO @ Fri, 26 Jun 2020 23:28:23: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:28:23: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:28:23: #1 total tags in treatment: 23052310 INFO @ Fri, 26 Jun 2020 23:28:23: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:28:23: #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 23:28:23: #1 tags after filtering in treatment: 23052238 INFO @ Fri, 26 Jun 2020 23:28:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:28:23: #1 finished! INFO @ Fri, 26 Jun 2020 23:28:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:28:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:28:25: #2 number of paired peaks: 537 WARNING @ Fri, 26 Jun 2020 23:28:25: Fewer paired peaks (537) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 537 pairs to build model! INFO @ Fri, 26 Jun 2020 23:28:25: start model_add_line... INFO @ Fri, 26 Jun 2020 23:28:25: start X-correlation... INFO @ Fri, 26 Jun 2020 23:28:25: end of X-cor INFO @ Fri, 26 Jun 2020 23:28:25: #2 finished! INFO @ Fri, 26 Jun 2020 23:28:25: #2 predicted fragment length is 102 bps INFO @ Fri, 26 Jun 2020 23:28:25: #2 alternative fragment length(s) may be 102 bps INFO @ Fri, 26 Jun 2020 23:28:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.20_model.r INFO @ Fri, 26 Jun 2020 23:28:25: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:28:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:28:43: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:29:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:29:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:29:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.10_summits.bed INFO @ Fri, 26 Jun 2020 23:29:06: Done! pass1 - making usageList (553 chroms): 1 millis pass2 - checking and writing primary data (2627 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:29:11: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:29:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:29:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:29:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2068662/SRX2068662.20_summits.bed INFO @ Fri, 26 Jun 2020 23:29:33: Done! pass1 - making usageList (477 chroms): 1 millis pass2 - checking and writing primary data (1972 records, 4 fields): 16 millis CompletedMACS2peakCalling