Job ID = 6451802 SRX = ERX011418 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:01:32 prefetch.2.10.7: 1) Downloading 'ERR031139'... 2020-06-21T07:01:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:03:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:03:52 prefetch.2.10.7: 'ERR031139' is valid 2020-06-21T07:03:52 prefetch.2.10.7: 1) 'ERR031139' was downloaded successfully 2020-06-21T07:04:44 prefetch.2.10.7: 'ERR031139' has 10 unresolved dependencies 2020-06-21T07:04:44 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.4?vdb-ctx=refseq'... 2020-06-21T07:04:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:05:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:05:00 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:05:00 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.5?vdb-ctx=refseq'... 2020-06-21T07:05:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:05:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:05:16 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:05:16 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.3?vdb-ctx=refseq'... 2020-06-21T07:05:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:05:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:05:29 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:05:29 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.4?vdb-ctx=refseq'... 2020-06-21T07:05:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:05:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:05:47 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:05:47 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.2?vdb-ctx=refseq'... 2020-06-21T07:05:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:06:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:06:04 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:06:04 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.4?vdb-ctx=refseq'... 2020-06-21T07:06:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:06:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:06:23 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:06:23 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CM000457.1?vdb-ctx=refseq'... 2020-06-21T07:06:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:06:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:06:36 prefetch.2.10.7: 8) 'ncbi-acc:CM000457.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:06:36 prefetch.2.10.7: 9) Downloading 'ncbi-acc:CM000458.1?vdb-ctx=refseq'... 2020-06-21T07:06:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:06:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:06:49 prefetch.2.10.7: 9) 'ncbi-acc:CM000458.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:06:49 prefetch.2.10.7: 10) Downloading 'ncbi-acc:CM000459.1?vdb-ctx=refseq'... 2020-06-21T07:06:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:07:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:07:02 prefetch.2.10.7: 10) 'ncbi-acc:CM000459.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:07:02 prefetch.2.10.7: 11) Downloading 'ncbi-acc:FA000001.1?vdb-ctx=refseq'... 2020-06-21T07:07:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:07:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:07:17 prefetch.2.10.7: 11) 'ncbi-acc:FA000001.1?vdb-ctx=refseq' was downloaded successfully Read 36475879 spots for ERR031139/ERR031139.sra Written 36475879 spots for ERR031139/ERR031139.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:16 36475879 reads; of these: 36475879 (100.00%) were unpaired; of these: 3534886 (9.69%) aligned 0 times 29671207 (81.34%) aligned exactly 1 time 3269786 (8.96%) aligned >1 times 90.31% overall alignment rate Time searching: 00:04:17 Overall time: 00:04:17 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 12 files... [bam_rmdupse_core] 21321168 / 32940993 = 0.6473 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 16:17:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.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 16:17:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:17:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:17:51: 1000000 INFO @ Sun, 21 Jun 2020 16:17:57: 2000000 INFO @ Sun, 21 Jun 2020 16:18:03: 3000000 INFO @ Sun, 21 Jun 2020 16:18:09: 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 16:18:15: 5000000 INFO @ Sun, 21 Jun 2020 16:18:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.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 16:18:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:18:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:18:21: 1000000 INFO @ Sun, 21 Jun 2020 16:18:21: 6000000 INFO @ Sun, 21 Jun 2020 16:18:26: 2000000 INFO @ Sun, 21 Jun 2020 16:18:27: 7000000 INFO @ Sun, 21 Jun 2020 16:18:32: 3000000 INFO @ Sun, 21 Jun 2020 16:18:33: 8000000 INFO @ Sun, 21 Jun 2020 16:18:38: 4000000 INFO @ Sun, 21 Jun 2020 16:18:40: 9000000 INFO @ Sun, 21 Jun 2020 16:18:43: 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 16:18:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.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 16:18:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:18:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:18:46: 10000000 INFO @ Sun, 21 Jun 2020 16:18:49: 6000000 INFO @ Sun, 21 Jun 2020 16:18:51: 1000000 INFO @ Sun, 21 Jun 2020 16:18:52: 11000000 INFO @ Sun, 21 Jun 2020 16:18:54: 7000000 INFO @ Sun, 21 Jun 2020 16:18:56: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:18:56: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:18:56: #1 total tags in treatment: 11619825 INFO @ Sun, 21 Jun 2020 16:18:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:18:56: #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 16:18:57: #1 tags after filtering in treatment: 11619751 INFO @ Sun, 21 Jun 2020 16:18:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:18:57: #1 finished! INFO @ Sun, 21 Jun 2020 16:18:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:18:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:18:57: 2000000 INFO @ Sun, 21 Jun 2020 16:18:58: #2 number of paired peaks: 5657 INFO @ Sun, 21 Jun 2020 16:18:58: start model_add_line... INFO @ Sun, 21 Jun 2020 16:18:58: start X-correlation... INFO @ Sun, 21 Jun 2020 16:18:58: end of X-cor INFO @ Sun, 21 Jun 2020 16:18:58: #2 finished! INFO @ Sun, 21 Jun 2020 16:18:58: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 16:18:58: #2 alternative fragment length(s) may be 4,58 bps INFO @ Sun, 21 Jun 2020 16:18:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.05_model.r WARNING @ Sun, 21 Jun 2020 16:18:58: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:18:58: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Sun, 21 Jun 2020 16:18:58: #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 16:18:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:18:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:19:00: 8000000 INFO @ Sun, 21 Jun 2020 16:19:03: 3000000 INFO @ Sun, 21 Jun 2020 16:19:06: 9000000 INFO @ Sun, 21 Jun 2020 16:19:09: 4000000 INFO @ Sun, 21 Jun 2020 16:19:12: 10000000 INFO @ Sun, 21 Jun 2020 16:19:15: 5000000 INFO @ Sun, 21 Jun 2020 16:19:18: 11000000 INFO @ Sun, 21 Jun 2020 16:19:21: 6000000 INFO @ Sun, 21 Jun 2020 16:19:22: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:19:22: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:19:22: #1 total tags in treatment: 11619825 INFO @ Sun, 21 Jun 2020 16:19:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:19:22: #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 16:19:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:19:22: #1 tags after filtering in treatment: 11619751 INFO @ Sun, 21 Jun 2020 16:19:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:19:22: #1 finished! INFO @ Sun, 21 Jun 2020 16:19:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:19:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:19:23: #2 number of paired peaks: 5657 INFO @ Sun, 21 Jun 2020 16:19:23: start model_add_line... INFO @ Sun, 21 Jun 2020 16:19:23: start X-correlation... INFO @ Sun, 21 Jun 2020 16:19:23: end of X-cor INFO @ Sun, 21 Jun 2020 16:19:23: #2 finished! INFO @ Sun, 21 Jun 2020 16:19:23: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 16:19:23: #2 alternative fragment length(s) may be 4,58 bps INFO @ Sun, 21 Jun 2020 16:19:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.10_model.r WARNING @ Sun, 21 Jun 2020 16:19:23: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:19:23: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Sun, 21 Jun 2020 16:19:23: #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 16:19:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:19:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:19:27: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:19:33: 8000000 INFO @ Sun, 21 Jun 2020 16:19:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:19:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:19:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.05_summits.bed INFO @ Sun, 21 Jun 2020 16:19:34: Done! pass1 - making usageList (331 chroms): 2 millis pass2 - checking and writing primary data (14075 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:19:38: 9000000 INFO @ Sun, 21 Jun 2020 16:19:44: 10000000 INFO @ Sun, 21 Jun 2020 16:19:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:19:50: 11000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:19:54: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:19:54: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:19:54: #1 total tags in treatment: 11619825 INFO @ Sun, 21 Jun 2020 16:19:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:19:54: #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 16:19:54: #1 tags after filtering in treatment: 11619751 INFO @ Sun, 21 Jun 2020 16:19:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:19:54: #1 finished! INFO @ Sun, 21 Jun 2020 16:19:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:19:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:19:55: #2 number of paired peaks: 5657 INFO @ Sun, 21 Jun 2020 16:19:55: start model_add_line... INFO @ Sun, 21 Jun 2020 16:19:55: start X-correlation... INFO @ Sun, 21 Jun 2020 16:19:55: end of X-cor INFO @ Sun, 21 Jun 2020 16:19:55: #2 finished! INFO @ Sun, 21 Jun 2020 16:19:55: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 16:19:55: #2 alternative fragment length(s) may be 4,58 bps INFO @ Sun, 21 Jun 2020 16:19:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.20_model.r WARNING @ Sun, 21 Jun 2020 16:19:55: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:19:55: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Sun, 21 Jun 2020 16:19:55: #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 16:19:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:19:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:20:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:20:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:20:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.10_summits.bed INFO @ Sun, 21 Jun 2020 16:20:01: Done! pass1 - making usageList (237 chroms): 1 millis pass2 - checking and writing primary data (5605 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:20:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:20:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:20:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:20:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011418/ERX011418.20_summits.bed INFO @ Sun, 21 Jun 2020 16:20:33: Done! pass1 - making usageList (125 chroms): 0 millis pass2 - checking and writing primary data (1250 records, 4 fields): 10 millis CompletedMACS2peakCalling