Job ID = 6451800 SRX = ERX011416 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:08:47 prefetch.2.10.7: 1) Downloading 'ERR031137'... 2020-06-21T07:08:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:10:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:10:59 prefetch.2.10.7: 'ERR031137' is valid 2020-06-21T07:10:59 prefetch.2.10.7: 1) 'ERR031137' was downloaded successfully 2020-06-21T07:11:51 prefetch.2.10.7: 'ERR031137' has 10 unresolved dependencies 2020-06-21T07:11:51 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.4?vdb-ctx=refseq'... 2020-06-21T07:11:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:12:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:12:11 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:12:11 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.5?vdb-ctx=refseq'... 2020-06-21T07:12:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:12:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:12:29 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:12:29 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.3?vdb-ctx=refseq'... 2020-06-21T07:12:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:12:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:12:41 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:12:41 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.4?vdb-ctx=refseq'... 2020-06-21T07:12:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:12:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:12:58 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:12:58 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.2?vdb-ctx=refseq'... 2020-06-21T07:12:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:13:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:13:17 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:13:17 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.4?vdb-ctx=refseq'... 2020-06-21T07:13:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:13:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:13:34 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:13:34 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CM000457.1?vdb-ctx=refseq'... 2020-06-21T07:13:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:13:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:13:47 prefetch.2.10.7: 8) 'ncbi-acc:CM000457.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:13:47 prefetch.2.10.7: 9) Downloading 'ncbi-acc:CM000458.1?vdb-ctx=refseq'... 2020-06-21T07:13:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:14:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:14:00 prefetch.2.10.7: 9) 'ncbi-acc:CM000458.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:14:00 prefetch.2.10.7: 10) Downloading 'ncbi-acc:CM000459.1?vdb-ctx=refseq'... 2020-06-21T07:14:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:14:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:14:13 prefetch.2.10.7: 10) 'ncbi-acc:CM000459.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:14:13 prefetch.2.10.7: 11) Downloading 'ncbi-acc:FA000001.1?vdb-ctx=refseq'... 2020-06-21T07:14:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:14:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:14:29 prefetch.2.10.7: 11) 'ncbi-acc:FA000001.1?vdb-ctx=refseq' was downloaded successfully Read 25379734 spots for ERR031137/ERR031137.sra Written 25379734 spots for ERR031137/ERR031137.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: 00:03:05 25379734 reads; of these: 25379734 (100.00%) were unpaired; of these: 597983 (2.36%) aligned 0 times 23247136 (91.60%) aligned exactly 1 time 1534615 (6.05%) aligned >1 times 97.64% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 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] 9818391 / 24781751 = 0.3962 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 16:24:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.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 16:24:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:24:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:24:14: 1000000 INFO @ Sun, 21 Jun 2020 16:24:18: 2000000 INFO @ Sun, 21 Jun 2020 16:24:23: 3000000 INFO @ Sun, 21 Jun 2020 16:24:28: 4000000 INFO @ Sun, 21 Jun 2020 16:24:33: 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 16:24:37: 6000000 INFO @ Sun, 21 Jun 2020 16:24:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.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 16:24:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:24:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:24:42: 7000000 INFO @ Sun, 21 Jun 2020 16:24:44: 1000000 INFO @ Sun, 21 Jun 2020 16:24:47: 8000000 INFO @ Sun, 21 Jun 2020 16:24:49: 2000000 INFO @ Sun, 21 Jun 2020 16:24:52: 9000000 INFO @ Sun, 21 Jun 2020 16:24:54: 3000000 INFO @ Sun, 21 Jun 2020 16:24:57: 10000000 INFO @ Sun, 21 Jun 2020 16:24:59: 4000000 INFO @ Sun, 21 Jun 2020 16:25:02: 11000000 INFO @ Sun, 21 Jun 2020 16:25:04: 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 16:25:08: 12000000 INFO @ Sun, 21 Jun 2020 16:25:09: 6000000 INFO @ Sun, 21 Jun 2020 16:25:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.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 16:25:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:25:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:25:13: 13000000 INFO @ Sun, 21 Jun 2020 16:25:14: 1000000 INFO @ Sun, 21 Jun 2020 16:25:14: 7000000 INFO @ Sun, 21 Jun 2020 16:25:19: 2000000 INFO @ Sun, 21 Jun 2020 16:25:19: 14000000 INFO @ Sun, 21 Jun 2020 16:25:19: 8000000 INFO @ Sun, 21 Jun 2020 16:25:23: 3000000 INFO @ Sun, 21 Jun 2020 16:25:24: 9000000 INFO @ Sun, 21 Jun 2020 16:25:24: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:25:24: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:25:24: #1 total tags in treatment: 14963360 INFO @ Sun, 21 Jun 2020 16:25:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:25:24: #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 16:25:25: #1 tags after filtering in treatment: 14963297 INFO @ Sun, 21 Jun 2020 16:25:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:25:25: #1 finished! INFO @ Sun, 21 Jun 2020 16:25:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:25:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:25:27: #2 number of paired peaks: 15271 INFO @ Sun, 21 Jun 2020 16:25:27: start model_add_line... INFO @ Sun, 21 Jun 2020 16:25:28: start X-correlation... INFO @ Sun, 21 Jun 2020 16:25:28: end of X-cor INFO @ Sun, 21 Jun 2020 16:25:28: #2 finished! INFO @ Sun, 21 Jun 2020 16:25:28: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 16:25:28: #2 alternative fragment length(s) may be 2,60 bps INFO @ Sun, 21 Jun 2020 16:25:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.05_model.r WARNING @ Sun, 21 Jun 2020 16:25:28: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:25:28: #2 You may need to consider one of the other alternative d(s): 2,60 WARNING @ Sun, 21 Jun 2020 16:25:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 16:25:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:25:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:25:28: 4000000 INFO @ Sun, 21 Jun 2020 16:25:29: 10000000 INFO @ Sun, 21 Jun 2020 16:25:32: 5000000 INFO @ Sun, 21 Jun 2020 16:25:34: 11000000 INFO @ Sun, 21 Jun 2020 16:25:37: 6000000 INFO @ Sun, 21 Jun 2020 16:25:38: 12000000 INFO @ Sun, 21 Jun 2020 16:25:42: 7000000 INFO @ Sun, 21 Jun 2020 16:25:44: 13000000 INFO @ Sun, 21 Jun 2020 16:25:46: 8000000 INFO @ Sun, 21 Jun 2020 16:25:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:25:49: 14000000 INFO @ Sun, 21 Jun 2020 16:25:51: 9000000 INFO @ Sun, 21 Jun 2020 16:25:55: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:25:55: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:25:55: #1 total tags in treatment: 14963360 INFO @ Sun, 21 Jun 2020 16:25:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:25:55: #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 16:25:55: #1 tags after filtering in treatment: 14963297 INFO @ Sun, 21 Jun 2020 16:25:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:25:55: #1 finished! INFO @ Sun, 21 Jun 2020 16:25:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:25:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:25:55: 10000000 INFO @ Sun, 21 Jun 2020 16:25:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:25:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:25:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.05_summits.bed INFO @ Sun, 21 Jun 2020 16:25:58: Done! INFO @ Sun, 21 Jun 2020 16:25:58: #2 number of paired peaks: 15271 INFO @ Sun, 21 Jun 2020 16:25:58: start model_add_line... pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:25:58: start X-correlation... INFO @ Sun, 21 Jun 2020 16:25:58: end of X-cor INFO @ Sun, 21 Jun 2020 16:25:58: #2 finished! INFO @ Sun, 21 Jun 2020 16:25:58: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 16:25:58: #2 alternative fragment length(s) may be 2,60 bps INFO @ Sun, 21 Jun 2020 16:25:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.10_model.r WARNING @ Sun, 21 Jun 2020 16:25:58: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:25:58: #2 You may need to consider one of the other alternative d(s): 2,60 WARNING @ Sun, 21 Jun 2020 16:25:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 16:25:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:25:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:26:00: 11000000 INFO @ Sun, 21 Jun 2020 16:26:04: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:26:09: 13000000 INFO @ Sun, 21 Jun 2020 16:26:14: 14000000 INFO @ Sun, 21 Jun 2020 16:26:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:26:19: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:26:19: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:26:19: #1 total tags in treatment: 14963360 INFO @ Sun, 21 Jun 2020 16:26:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:26:19: #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 16:26:19: #1 tags after filtering in treatment: 14963297 INFO @ Sun, 21 Jun 2020 16:26:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:26:19: #1 finished! INFO @ Sun, 21 Jun 2020 16:26:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:26:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:26:22: #2 number of paired peaks: 15271 INFO @ Sun, 21 Jun 2020 16:26:22: start model_add_line... INFO @ Sun, 21 Jun 2020 16:26:22: start X-correlation... INFO @ Sun, 21 Jun 2020 16:26:22: end of X-cor INFO @ Sun, 21 Jun 2020 16:26:22: #2 finished! INFO @ Sun, 21 Jun 2020 16:26:22: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 16:26:22: #2 alternative fragment length(s) may be 2,60 bps INFO @ Sun, 21 Jun 2020 16:26:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.20_model.r WARNING @ Sun, 21 Jun 2020 16:26:22: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:26:22: #2 You may need to consider one of the other alternative d(s): 2,60 WARNING @ Sun, 21 Jun 2020 16:26:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 16:26:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:26:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:26:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:26:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:26:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.10_summits.bed INFO @ Sun, 21 Jun 2020 16:26:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:26:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:26:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:26:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:26:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011416/ERX011416.20_summits.bed INFO @ Sun, 21 Jun 2020 16:26:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling