Job ID = 6455843 SRX = SRX3011249 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:20:51 prefetch.2.10.7: 1) Downloading 'SRR5834726'... 2020-06-21T10:20:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:02 prefetch.2.10.7: 'SRR5834726' is valid 2020-06-21T10:23:02 prefetch.2.10.7: 1) 'SRR5834726' was downloaded successfully 2020-06-21T10:23:53 prefetch.2.10.7: 'SRR5834726' has 10 unresolved dependencies 2020-06-21T10:23:53 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T10:23:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:24:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:24:05 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:24:05 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T10:24:05 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: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:24:28 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?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: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:24:45 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T10:24:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:25:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:25:05 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:25:05 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T10:25:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:25:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:25:22 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:25:22 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T10:25:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:25:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:25:38 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:25:38 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T10:25:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:25:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:25:54 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:25:54 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T10:25:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:26:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:26:09 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:26:09 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T10:26:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:26:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:26:22 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:26:22 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T10:26:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:26:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:26:36 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 16318116 spots for SRR5834726/SRR5834726.sra Written 16318116 spots for SRR5834726/SRR5834726.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: 00:04:46 16318116 reads; of these: 16318116 (100.00%) were unpaired; of these: 275389 (1.69%) aligned 0 times 12215613 (74.86%) aligned exactly 1 time 3827114 (23.45%) aligned >1 times 98.31% overall alignment rate Time searching: 00:04:46 Overall time: 00:04:46 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] 6511753 / 16042727 = 0.4059 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 19:36:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.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 19:36:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:36:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:37:01: 1000000 INFO @ Sun, 21 Jun 2020 19:37:09: 2000000 INFO @ Sun, 21 Jun 2020 19:37:16: 3000000 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 19:37:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.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 19:37:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:37:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:37:24: 4000000 INFO @ Sun, 21 Jun 2020 19:37:31: 1000000 INFO @ Sun, 21 Jun 2020 19:37:33: 5000000 INFO @ Sun, 21 Jun 2020 19:37:39: 2000000 INFO @ Sun, 21 Jun 2020 19:37:42: 6000000 INFO @ Sun, 21 Jun 2020 19:37:48: 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 19:37:51: 7000000 INFO @ Sun, 21 Jun 2020 19:37:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.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 19:37:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:37:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:37:56: 4000000 INFO @ Sun, 21 Jun 2020 19:38:00: 8000000 INFO @ Sun, 21 Jun 2020 19:38:01: 1000000 INFO @ Sun, 21 Jun 2020 19:38:05: 5000000 INFO @ Sun, 21 Jun 2020 19:38:09: 9000000 INFO @ Sun, 21 Jun 2020 19:38:10: 2000000 INFO @ Sun, 21 Jun 2020 19:38:13: 6000000 INFO @ Sun, 21 Jun 2020 19:38:14: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:38:14: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:38:14: #1 total tags in treatment: 9530974 INFO @ Sun, 21 Jun 2020 19:38:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:38:14: #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 19:38:15: #1 tags after filtering in treatment: 9530835 INFO @ Sun, 21 Jun 2020 19:38:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:38:15: #1 finished! INFO @ Sun, 21 Jun 2020 19:38:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:38:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:38:16: #2 number of paired peaks: 2276 INFO @ Sun, 21 Jun 2020 19:38:16: start model_add_line... INFO @ Sun, 21 Jun 2020 19:38:16: start X-correlation... INFO @ Sun, 21 Jun 2020 19:38:16: end of X-cor INFO @ Sun, 21 Jun 2020 19:38:16: #2 finished! INFO @ Sun, 21 Jun 2020 19:38:16: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 19:38:16: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 19:38:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.05_model.r WARNING @ Sun, 21 Jun 2020 19:38:16: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:38:16: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Sun, 21 Jun 2020 19:38:16: #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 19:38:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:38:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:38:19: 3000000 INFO @ Sun, 21 Jun 2020 19:38:21: 7000000 INFO @ Sun, 21 Jun 2020 19:38:27: 4000000 INFO @ Sun, 21 Jun 2020 19:38:30: 8000000 INFO @ Sun, 21 Jun 2020 19:38:36: 5000000 INFO @ Sun, 21 Jun 2020 19:38:39: 9000000 INFO @ Sun, 21 Jun 2020 19:38:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:38:43: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:38:43: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:38:43: #1 total tags in treatment: 9530974 INFO @ Sun, 21 Jun 2020 19:38:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:38:43: #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 19:38:43: #1 tags after filtering in treatment: 9530835 INFO @ Sun, 21 Jun 2020 19:38:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:38:43: #1 finished! INFO @ Sun, 21 Jun 2020 19:38:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:38:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:38:44: #2 number of paired peaks: 2276 INFO @ Sun, 21 Jun 2020 19:38:44: start model_add_line... INFO @ Sun, 21 Jun 2020 19:38:44: start X-correlation... INFO @ Sun, 21 Jun 2020 19:38:44: end of X-cor INFO @ Sun, 21 Jun 2020 19:38:44: #2 finished! INFO @ Sun, 21 Jun 2020 19:38:44: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 19:38:44: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 19:38:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.10_model.r WARNING @ Sun, 21 Jun 2020 19:38:44: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:38:44: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Sun, 21 Jun 2020 19:38:44: #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 19:38:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:38:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:38:44: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:38:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.05_summits.bed INFO @ Sun, 21 Jun 2020 19:38:51: Done! pass1 - making usageList (516 chroms): 2 millis pass2 - checking and writing primary data (7966 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:38:53: 7000000 INFO @ Sun, 21 Jun 2020 19:39:01: 8000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:39:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:39:09: 9000000 INFO @ Sun, 21 Jun 2020 19:39:13: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:39:13: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:39:13: #1 total tags in treatment: 9530974 INFO @ Sun, 21 Jun 2020 19:39:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:39:13: #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 19:39:13: #1 tags after filtering in treatment: 9530835 INFO @ Sun, 21 Jun 2020 19:39:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:39:13: #1 finished! INFO @ Sun, 21 Jun 2020 19:39:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:39:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:39:14: #2 number of paired peaks: 2276 INFO @ Sun, 21 Jun 2020 19:39:14: start model_add_line... INFO @ Sun, 21 Jun 2020 19:39:14: start X-correlation... INFO @ Sun, 21 Jun 2020 19:39:14: end of X-cor INFO @ Sun, 21 Jun 2020 19:39:14: #2 finished! INFO @ Sun, 21 Jun 2020 19:39:14: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 19:39:14: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 19:39:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.20_model.r WARNING @ Sun, 21 Jun 2020 19:39:14: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:39:14: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Sun, 21 Jun 2020 19:39:14: #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 19:39:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:39:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:39:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:39:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:39:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.10_summits.bed INFO @ Sun, 21 Jun 2020 19:39:18: Done! pass1 - making usageList (386 chroms): 1 millis pass2 - checking and writing primary data (4601 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:39:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:39:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:39:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:39:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011249/SRX3011249.20_summits.bed INFO @ Sun, 21 Jun 2020 19:39:49: Done! pass1 - making usageList (226 chroms): 1 millis pass2 - checking and writing primary data (1923 records, 4 fields): 9 millis CompletedMACS2peakCalling