Job ID = 6455853 SRX = SRX3011257 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:17:36 prefetch.2.10.7: 1) Downloading 'SRR5834734'... 2020-06-21T10:17:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:55 prefetch.2.10.7: 1) 'SRR5834734' was downloaded successfully 2020-06-21T10:22:47 prefetch.2.10.7: 'SRR5834734' has 10 unresolved dependencies 2020-06-21T10:22:47 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T10:22:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:58 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:22:58 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T10:22:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:14 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:23:14 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T10:23:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:29 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:23:29 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T10:23:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:51 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:23:51 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T10:23:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:24:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:24:11 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:24:11 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T10:24:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:24:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:24:28 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:24:28 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T10:24:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:24:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:24:45 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:24:45 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T10:24:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:24:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:24:58 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:24:58 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T10:24:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:25:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:25:26 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:25:26 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T10:25:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:25:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:25:40 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 30637517 spots for SRR5834734/SRR5834734.sra Written 30637517 spots for SRR5834734/SRR5834734.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: 00:04:24 30637517 reads; of these: 30637517 (100.00%) were unpaired; of these: 409280 (1.34%) aligned 0 times 29510194 (96.32%) aligned exactly 1 time 718043 (2.34%) aligned >1 times 98.66% overall alignment rate Time searching: 00:04:24 Overall time: 00:04:24 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] 5785658 / 30228237 = 0.1914 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 19:39:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.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 19:39:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:39:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:39:13: 1000000 INFO @ Sun, 21 Jun 2020 19:39:19: 2000000 INFO @ Sun, 21 Jun 2020 19:39:25: 3000000 INFO @ Sun, 21 Jun 2020 19:39:31: 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 19:39:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.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 19:39:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:39:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:39:37: 5000000 INFO @ Sun, 21 Jun 2020 19:39:43: 1000000 INFO @ Sun, 21 Jun 2020 19:39:43: 6000000 INFO @ Sun, 21 Jun 2020 19:39:49: 7000000 INFO @ Sun, 21 Jun 2020 19:39:49: 2000000 INFO @ Sun, 21 Jun 2020 19:39:56: 8000000 INFO @ Sun, 21 Jun 2020 19:39:56: 3000000 INFO @ Sun, 21 Jun 2020 19:40:02: 9000000 INFO @ Sun, 21 Jun 2020 19:40:02: 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 19:40:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.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 19:40:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:40:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:40:08: 10000000 INFO @ Sun, 21 Jun 2020 19:40:09: 5000000 INFO @ Sun, 21 Jun 2020 19:40:13: 1000000 INFO @ Sun, 21 Jun 2020 19:40:15: 11000000 INFO @ Sun, 21 Jun 2020 19:40:15: 6000000 INFO @ Sun, 21 Jun 2020 19:40:20: 2000000 INFO @ Sun, 21 Jun 2020 19:40:22: 12000000 INFO @ Sun, 21 Jun 2020 19:40:22: 7000000 INFO @ Sun, 21 Jun 2020 19:40:26: 3000000 INFO @ Sun, 21 Jun 2020 19:40:28: 13000000 INFO @ Sun, 21 Jun 2020 19:40:29: 8000000 INFO @ Sun, 21 Jun 2020 19:40:33: 4000000 INFO @ Sun, 21 Jun 2020 19:40:35: 14000000 INFO @ Sun, 21 Jun 2020 19:40:35: 9000000 INFO @ Sun, 21 Jun 2020 19:40:39: 5000000 INFO @ Sun, 21 Jun 2020 19:40:42: 15000000 INFO @ Sun, 21 Jun 2020 19:40:42: 10000000 INFO @ Sun, 21 Jun 2020 19:40:46: 6000000 INFO @ Sun, 21 Jun 2020 19:40:48: 16000000 INFO @ Sun, 21 Jun 2020 19:40:48: 11000000 INFO @ Sun, 21 Jun 2020 19:40:52: 7000000 INFO @ Sun, 21 Jun 2020 19:40:55: 17000000 INFO @ Sun, 21 Jun 2020 19:40:55: 12000000 INFO @ Sun, 21 Jun 2020 19:40:59: 8000000 INFO @ Sun, 21 Jun 2020 19:41:01: 18000000 INFO @ Sun, 21 Jun 2020 19:41:02: 13000000 INFO @ Sun, 21 Jun 2020 19:41:05: 9000000 INFO @ Sun, 21 Jun 2020 19:41:08: 19000000 INFO @ Sun, 21 Jun 2020 19:41:08: 14000000 INFO @ Sun, 21 Jun 2020 19:41:12: 10000000 INFO @ Sun, 21 Jun 2020 19:41:14: 20000000 INFO @ Sun, 21 Jun 2020 19:41:15: 15000000 INFO @ Sun, 21 Jun 2020 19:41:18: 11000000 INFO @ Sun, 21 Jun 2020 19:41:21: 21000000 INFO @ Sun, 21 Jun 2020 19:41:22: 16000000 INFO @ Sun, 21 Jun 2020 19:41:25: 12000000 INFO @ Sun, 21 Jun 2020 19:41:28: 22000000 INFO @ Sun, 21 Jun 2020 19:41:28: 17000000 INFO @ Sun, 21 Jun 2020 19:41:32: 13000000 INFO @ Sun, 21 Jun 2020 19:41:35: 23000000 INFO @ Sun, 21 Jun 2020 19:41:35: 18000000 INFO @ Sun, 21 Jun 2020 19:41:38: 14000000 INFO @ Sun, 21 Jun 2020 19:41:41: 24000000 INFO @ Sun, 21 Jun 2020 19:41:41: 19000000 INFO @ Sun, 21 Jun 2020 19:41:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:41:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:41:45: #1 total tags in treatment: 24442579 INFO @ Sun, 21 Jun 2020 19:41:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:41:45: #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 19:41:45: 15000000 INFO @ Sun, 21 Jun 2020 19:41:45: #1 tags after filtering in treatment: 24442195 INFO @ Sun, 21 Jun 2020 19:41:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:41:45: #1 finished! INFO @ Sun, 21 Jun 2020 19:41:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:41:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:41:47: #2 number of paired peaks: 110 WARNING @ Sun, 21 Jun 2020 19:41:47: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sun, 21 Jun 2020 19:41:47: start model_add_line... INFO @ Sun, 21 Jun 2020 19:41:47: start X-correlation... INFO @ Sun, 21 Jun 2020 19:41:47: end of X-cor INFO @ Sun, 21 Jun 2020 19:41:47: #2 finished! INFO @ Sun, 21 Jun 2020 19:41:47: #2 predicted fragment length is 149 bps INFO @ Sun, 21 Jun 2020 19:41:47: #2 alternative fragment length(s) may be 4,64,136,149,167 bps INFO @ Sun, 21 Jun 2020 19:41:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.05_model.r INFO @ Sun, 21 Jun 2020 19:41:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:41:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:41:48: 20000000 INFO @ Sun, 21 Jun 2020 19:41:51: 16000000 INFO @ Sun, 21 Jun 2020 19:41:55: 21000000 INFO @ Sun, 21 Jun 2020 19:41:58: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:42:01: 22000000 INFO @ Sun, 21 Jun 2020 19:42:04: 18000000 INFO @ Sun, 21 Jun 2020 19:42:08: 23000000 INFO @ Sun, 21 Jun 2020 19:42:10: 19000000 INFO @ Sun, 21 Jun 2020 19:42:15: 24000000 INFO @ Sun, 21 Jun 2020 19:42:17: 20000000 INFO @ Sun, 21 Jun 2020 19:42:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:42:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:42:18: #1 total tags in treatment: 24442579 INFO @ Sun, 21 Jun 2020 19:42:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:42:18: #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 19:42:18: #1 tags after filtering in treatment: 24442195 INFO @ Sun, 21 Jun 2020 19:42:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:42:18: #1 finished! INFO @ Sun, 21 Jun 2020 19:42:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:42:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:42:20: #2 number of paired peaks: 110 WARNING @ Sun, 21 Jun 2020 19:42:20: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sun, 21 Jun 2020 19:42:20: start model_add_line... INFO @ Sun, 21 Jun 2020 19:42:20: start X-correlation... INFO @ Sun, 21 Jun 2020 19:42:20: end of X-cor INFO @ Sun, 21 Jun 2020 19:42:20: #2 finished! INFO @ Sun, 21 Jun 2020 19:42:20: #2 predicted fragment length is 149 bps INFO @ Sun, 21 Jun 2020 19:42:20: #2 alternative fragment length(s) may be 4,64,136,149,167 bps INFO @ Sun, 21 Jun 2020 19:42:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.10_model.r INFO @ Sun, 21 Jun 2020 19:42:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:42:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:42:23: 21000000 INFO @ Sun, 21 Jun 2020 19:42:29: 22000000 INFO @ Sun, 21 Jun 2020 19:42:35: 23000000 INFO @ Sun, 21 Jun 2020 19:42:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:42:41: 24000000 INFO @ Sun, 21 Jun 2020 19:42:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:42:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:42:44: #1 total tags in treatment: 24442579 INFO @ Sun, 21 Jun 2020 19:42:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:42:44: #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 19:42:45: #1 tags after filtering in treatment: 24442195 INFO @ Sun, 21 Jun 2020 19:42:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:42:45: #1 finished! INFO @ Sun, 21 Jun 2020 19:42:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:42:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:42:47: #2 number of paired peaks: 110 WARNING @ Sun, 21 Jun 2020 19:42:47: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sun, 21 Jun 2020 19:42:47: start model_add_line... INFO @ Sun, 21 Jun 2020 19:42:47: start X-correlation... INFO @ Sun, 21 Jun 2020 19:42:47: end of X-cor INFO @ Sun, 21 Jun 2020 19:42:47: #2 finished! INFO @ Sun, 21 Jun 2020 19:42:47: #2 predicted fragment length is 149 bps INFO @ Sun, 21 Jun 2020 19:42:47: #2 alternative fragment length(s) may be 4,64,136,149,167 bps INFO @ Sun, 21 Jun 2020 19:42:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.20_model.r INFO @ Sun, 21 Jun 2020 19:42:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:42:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:43:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:43:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:43:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.05_summits.bed INFO @ Sun, 21 Jun 2020 19:43:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5144 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:43:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:43:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:43:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:43:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.10_summits.bed INFO @ Sun, 21 Jun 2020 19:43:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1214 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:43:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:44:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:44:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:44:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011257/SRX3011257.20_summits.bed INFO @ Sun, 21 Jun 2020 19:44:02: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (99 records, 4 fields): 2 millis CompletedMACS2peakCalling