Job ID = 6455827 SRX = SRX3011234 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:28:51 prefetch.2.10.7: 1) Downloading 'SRR5834711'... 2020-06-21T10:28:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:30:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:30:51 prefetch.2.10.7: 'SRR5834711' is valid 2020-06-21T10:30:51 prefetch.2.10.7: 1) 'SRR5834711' was downloaded successfully 2020-06-21T10:31:42 prefetch.2.10.7: 'SRR5834711' has 10 unresolved dependencies 2020-06-21T10:31:42 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T10:31:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:31:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:31:55 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:31:55 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T10:31:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:32:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:32:12 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:32:12 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T10:32:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:32:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:32:28 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:32:28 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T10:32:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:32:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:32:45 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:32:45 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T10:32:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:33:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:33:01 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:33:01 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T10:33:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:33:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:33:17 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:33:17 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T10:33:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:33:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:33:35 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:33:35 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T10:33:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:33:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:33:48 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:33:48 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T10:33:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:34:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:34:01 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:34:01 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T10:34:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:34:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:34:13 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 27248679 spots for SRR5834711/SRR5834711.sra Written 27248679 spots for SRR5834711/SRR5834711.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: 00:04:14 27248679 reads; of these: 27248679 (100.00%) were unpaired; of these: 14273347 (52.38%) aligned 0 times 9058339 (33.24%) aligned exactly 1 time 3916993 (14.37%) aligned >1 times 47.62% overall alignment rate Time searching: 00:04:14 Overall time: 00:04:14 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] 6136382 / 12975332 = 0.4729 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 19:42:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.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 19:42:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:42:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:42:20: 1000000 INFO @ Sun, 21 Jun 2020 19:42:27: 2000000 INFO @ Sun, 21 Jun 2020 19:42:34: 3000000 INFO @ Sun, 21 Jun 2020 19:42:41: 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 19:42:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.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 19:42:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:42:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:42:49: 5000000 INFO @ Sun, 21 Jun 2020 19:42:51: 1000000 INFO @ Sun, 21 Jun 2020 19:42:58: 6000000 INFO @ Sun, 21 Jun 2020 19:42:59: 2000000 INFO @ Sun, 21 Jun 2020 19:43:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:43:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:43:05: #1 total tags in treatment: 6838950 INFO @ Sun, 21 Jun 2020 19:43:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:43:05: #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 19:43:05: #1 tags after filtering in treatment: 6838769 INFO @ Sun, 21 Jun 2020 19:43:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:43:05: #1 finished! INFO @ Sun, 21 Jun 2020 19:43:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:43:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:43:06: #2 number of paired peaks: 2942 INFO @ Sun, 21 Jun 2020 19:43:06: start model_add_line... INFO @ Sun, 21 Jun 2020 19:43:06: start X-correlation... INFO @ Sun, 21 Jun 2020 19:43:06: end of X-cor INFO @ Sun, 21 Jun 2020 19:43:06: #2 finished! INFO @ Sun, 21 Jun 2020 19:43:06: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 19:43:06: #2 alternative fragment length(s) may be 84 bps INFO @ Sun, 21 Jun 2020 19:43:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.05_model.r WARNING @ Sun, 21 Jun 2020 19:43:06: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:43:06: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sun, 21 Jun 2020 19:43:06: #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 19:43:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:43:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:43:07: 3000000 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 19:43:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.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 19:43:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:43:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:43:14: 4000000 INFO @ Sun, 21 Jun 2020 19:43:22: 1000000 INFO @ Sun, 21 Jun 2020 19:43:22: 5000000 INFO @ Sun, 21 Jun 2020 19:43:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:43:29: 2000000 INFO @ Sun, 21 Jun 2020 19:43:30: 6000000 INFO @ Sun, 21 Jun 2020 19:43:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:43:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:43:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.05_summits.bed INFO @ Sun, 21 Jun 2020 19:43:31: Done! pass1 - making usageList (569 chroms): 2 millis pass2 - checking and writing primary data (4361 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:43:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:43:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:43:37: #1 total tags in treatment: 6838950 INFO @ Sun, 21 Jun 2020 19:43:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:43:37: #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 19:43:37: 3000000 INFO @ Sun, 21 Jun 2020 19:43:37: #1 tags after filtering in treatment: 6838769 INFO @ Sun, 21 Jun 2020 19:43:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:43:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:43:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:43:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:43:38: #2 number of paired peaks: 2942 INFO @ Sun, 21 Jun 2020 19:43:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:43:38: start X-correlation... INFO @ Sun, 21 Jun 2020 19:43:38: end of X-cor INFO @ Sun, 21 Jun 2020 19:43:38: #2 finished! INFO @ Sun, 21 Jun 2020 19:43:38: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 19:43:38: #2 alternative fragment length(s) may be 84 bps INFO @ Sun, 21 Jun 2020 19:43:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.10_model.r WARNING @ Sun, 21 Jun 2020 19:43:38: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:43:38: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sun, 21 Jun 2020 19:43:38: #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 19:43:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:43:38: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:43:44: 4000000 INFO @ Sun, 21 Jun 2020 19:43:51: 5000000 INFO @ Sun, 21 Jun 2020 19:43:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:43:59: 6000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:44:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:44:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:44:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.10_summits.bed INFO @ Sun, 21 Jun 2020 19:44:02: Done! pass1 - making usageList (484 chroms): 2 millis pass2 - checking and writing primary data (2493 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:44:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:44:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:44:04: #1 total tags in treatment: 6838950 INFO @ Sun, 21 Jun 2020 19:44:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:44:04: #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 19:44:05: #1 tags after filtering in treatment: 6838769 INFO @ Sun, 21 Jun 2020 19:44:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:44:05: #1 finished! INFO @ Sun, 21 Jun 2020 19:44:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:44:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:44:05: #2 number of paired peaks: 2942 INFO @ Sun, 21 Jun 2020 19:44:05: start model_add_line... INFO @ Sun, 21 Jun 2020 19:44:05: start X-correlation... INFO @ Sun, 21 Jun 2020 19:44:05: end of X-cor INFO @ Sun, 21 Jun 2020 19:44:05: #2 finished! INFO @ Sun, 21 Jun 2020 19:44:05: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 19:44:05: #2 alternative fragment length(s) may be 84 bps INFO @ Sun, 21 Jun 2020 19:44:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.20_model.r WARNING @ Sun, 21 Jun 2020 19:44:05: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:44:05: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sun, 21 Jun 2020 19:44:05: #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 19:44:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:44:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:44:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:44:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:44:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:44:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011234/SRX3011234.20_summits.bed INFO @ Sun, 21 Jun 2020 19:44:28: Done! pass1 - making usageList (230 chroms): 2 millis pass2 - checking and writing primary data (915 records, 4 fields): 7 millis CompletedMACS2peakCalling