Job ID = 6455856 SRX = SRX3011267 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:29:21 prefetch.2.10.7: 1) Downloading 'SRR5834743'... 2020-06-21T10:29:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:31:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:31:36 prefetch.2.10.7: 1) 'SRR5834743' was downloaded successfully 2020-06-21T10:32:27 prefetch.2.10.7: 'SRR5834743' has 10 unresolved dependencies 2020-06-21T10:32:27 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T10:32:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:32:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:32:40 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:32:40 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T10:32:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:32:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:32:55 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:32:55 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T10:32:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:33:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:33:10 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:33:10 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T10:33:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:33:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:33:27 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:33:27 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T10:33:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:33:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:33:45 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:33:45 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T10:33:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:34:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:34:06 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:34:06 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T10:34:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:34:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:34:24 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:34:24 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T10:34:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:34:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:34:38 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:34:38 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T10:34:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:34:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:34:52 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:34:52 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T10:34:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:35:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:35:05 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 37493028 spots for SRR5834743/SRR5834743.sra Written 37493028 spots for SRR5834743/SRR5834743.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: 00:06:03 37493028 reads; of these: 37493028 (100.00%) were unpaired; of these: 6389473 (17.04%) aligned 0 times 23820472 (63.53%) aligned exactly 1 time 7283083 (19.43%) aligned >1 times 82.96% overall alignment rate Time searching: 00:06:03 Overall time: 00:06:03 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] 8767936 / 31103555 = 0.2819 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 19:48:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.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 19:48:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:48:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:48:35: 1000000 INFO @ Sun, 21 Jun 2020 19:48:41: 2000000 INFO @ Sun, 21 Jun 2020 19:48:46: 3000000 INFO @ Sun, 21 Jun 2020 19:48:51: 4000000 INFO @ Sun, 21 Jun 2020 19:48:56: 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 19:49:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.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 19:49:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:49:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:49:01: 6000000 INFO @ Sun, 21 Jun 2020 19:49:05: 1000000 INFO @ Sun, 21 Jun 2020 19:49:06: 7000000 INFO @ Sun, 21 Jun 2020 19:49:10: 2000000 INFO @ Sun, 21 Jun 2020 19:49:11: 8000000 INFO @ Sun, 21 Jun 2020 19:49:15: 3000000 INFO @ Sun, 21 Jun 2020 19:49:16: 9000000 INFO @ Sun, 21 Jun 2020 19:49:21: 4000000 INFO @ Sun, 21 Jun 2020 19:49:21: 10000000 INFO @ Sun, 21 Jun 2020 19:49:26: 5000000 INFO @ Sun, 21 Jun 2020 19:49:26: 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 19:49:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.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 19:49:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:49:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:49:31: 6000000 INFO @ Sun, 21 Jun 2020 19:49:31: 12000000 INFO @ Sun, 21 Jun 2020 19:49:34: 1000000 INFO @ Sun, 21 Jun 2020 19:49:36: 7000000 INFO @ Sun, 21 Jun 2020 19:49:37: 13000000 INFO @ Sun, 21 Jun 2020 19:49:39: 2000000 INFO @ Sun, 21 Jun 2020 19:49:41: 8000000 INFO @ Sun, 21 Jun 2020 19:49:42: 14000000 INFO @ Sun, 21 Jun 2020 19:49:44: 3000000 INFO @ Sun, 21 Jun 2020 19:49:46: 9000000 INFO @ Sun, 21 Jun 2020 19:49:47: 15000000 INFO @ Sun, 21 Jun 2020 19:49:48: 4000000 INFO @ Sun, 21 Jun 2020 19:49:51: 10000000 INFO @ Sun, 21 Jun 2020 19:49:52: 16000000 INFO @ Sun, 21 Jun 2020 19:49:53: 5000000 INFO @ Sun, 21 Jun 2020 19:49:56: 11000000 INFO @ Sun, 21 Jun 2020 19:49:57: 17000000 INFO @ Sun, 21 Jun 2020 19:49:57: 6000000 INFO @ Sun, 21 Jun 2020 19:50:01: 12000000 INFO @ Sun, 21 Jun 2020 19:50:02: 7000000 INFO @ Sun, 21 Jun 2020 19:50:03: 18000000 INFO @ Sun, 21 Jun 2020 19:50:06: 13000000 INFO @ Sun, 21 Jun 2020 19:50:06: 8000000 INFO @ Sun, 21 Jun 2020 19:50:08: 19000000 INFO @ Sun, 21 Jun 2020 19:50:11: 9000000 INFO @ Sun, 21 Jun 2020 19:50:11: 14000000 INFO @ Sun, 21 Jun 2020 19:50:13: 20000000 INFO @ Sun, 21 Jun 2020 19:50:15: 10000000 INFO @ Sun, 21 Jun 2020 19:50:17: 15000000 INFO @ Sun, 21 Jun 2020 19:50:18: 21000000 INFO @ Sun, 21 Jun 2020 19:50:20: 11000000 INFO @ Sun, 21 Jun 2020 19:50:22: 16000000 INFO @ Sun, 21 Jun 2020 19:50:23: 22000000 INFO @ Sun, 21 Jun 2020 19:50:25: 12000000 INFO @ Sun, 21 Jun 2020 19:50:25: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 19:50:25: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 19:50:25: #1 total tags in treatment: 22335619 INFO @ Sun, 21 Jun 2020 19:50:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:25: #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 19:50:26: #1 tags after filtering in treatment: 22335555 INFO @ Sun, 21 Jun 2020 19:50:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:26: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:27: 17000000 INFO @ Sun, 21 Jun 2020 19:50:27: #2 number of paired peaks: 954 WARNING @ Sun, 21 Jun 2020 19:50:27: Fewer paired peaks (954) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 954 pairs to build model! INFO @ Sun, 21 Jun 2020 19:50:27: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:28: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:28: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:28: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:28: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 19:50:28: #2 alternative fragment length(s) may be 126 bps INFO @ Sun, 21 Jun 2020 19:50:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.05_model.r INFO @ Sun, 21 Jun 2020 19:50:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:50:29: 13000000 INFO @ Sun, 21 Jun 2020 19:50:32: 18000000 INFO @ Sun, 21 Jun 2020 19:50:34: 14000000 INFO @ Sun, 21 Jun 2020 19:50:37: 19000000 INFO @ Sun, 21 Jun 2020 19:50:38: 15000000 INFO @ Sun, 21 Jun 2020 19:50:43: 20000000 INFO @ Sun, 21 Jun 2020 19:50:43: 16000000 INFO @ Sun, 21 Jun 2020 19:50:47: 17000000 INFO @ Sun, 21 Jun 2020 19:50:48: 21000000 INFO @ Sun, 21 Jun 2020 19:50:52: 18000000 INFO @ Sun, 21 Jun 2020 19:50:53: 22000000 INFO @ Sun, 21 Jun 2020 19:50:55: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 19:50:55: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 19:50:55: #1 total tags in treatment: 22335619 INFO @ Sun, 21 Jun 2020 19:50:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:55: #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 19:50:56: #1 tags after filtering in treatment: 22335555 INFO @ Sun, 21 Jun 2020 19:50:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:56: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:57: 19000000 INFO @ Sun, 21 Jun 2020 19:50:57: #2 number of paired peaks: 954 WARNING @ Sun, 21 Jun 2020 19:50:57: Fewer paired peaks (954) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 954 pairs to build model! INFO @ Sun, 21 Jun 2020 19:50:57: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:57: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:57: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:57: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:57: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 19:50:57: #2 alternative fragment length(s) may be 126 bps INFO @ Sun, 21 Jun 2020 19:50:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.10_model.r INFO @ Sun, 21 Jun 2020 19:50:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:51:01: 20000000 INFO @ Sun, 21 Jun 2020 19:51:06: 21000000 INFO @ Sun, 21 Jun 2020 19:51:10: 22000000 INFO @ Sun, 21 Jun 2020 19:51:12: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 19:51:12: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 19:51:12: #1 total tags in treatment: 22335619 INFO @ Sun, 21 Jun 2020 19:51:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:51:12: #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 19:51:13: #1 tags after filtering in treatment: 22335555 INFO @ Sun, 21 Jun 2020 19:51:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:51:13: #1 finished! INFO @ Sun, 21 Jun 2020 19:51:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:51:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:51:14: #2 number of paired peaks: 954 WARNING @ Sun, 21 Jun 2020 19:51:14: Fewer paired peaks (954) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 954 pairs to build model! INFO @ Sun, 21 Jun 2020 19:51:14: start model_add_line... INFO @ Sun, 21 Jun 2020 19:51:14: start X-correlation... INFO @ Sun, 21 Jun 2020 19:51:14: end of X-cor INFO @ Sun, 21 Jun 2020 19:51:14: #2 finished! INFO @ Sun, 21 Jun 2020 19:51:14: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 19:51:14: #2 alternative fragment length(s) may be 126 bps INFO @ Sun, 21 Jun 2020 19:51:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.20_model.r INFO @ Sun, 21 Jun 2020 19:51:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:51:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:51:14: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:51:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:51:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:51:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.05_summits.bed INFO @ Sun, 21 Jun 2020 19:51:38: Done! pass1 - making usageList (582 chroms): 3 millis pass2 - checking and writing primary data (12204 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:51:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:52:02: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:52:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:52:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:52:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.10_summits.bed INFO @ Sun, 21 Jun 2020 19:52:08: Done! pass1 - making usageList (470 chroms): 1 millis pass2 - checking and writing primary data (7420 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:52:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:52:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:52:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011267/SRX3011267.20_summits.bed INFO @ Sun, 21 Jun 2020 19:52:26: Done! pass1 - making usageList (248 chroms): 1 millis pass2 - checking and writing primary data (2868 records, 4 fields): 11 millis CompletedMACS2peakCalling