Job ID = 6453442 SRX = SRX1149359 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:13:03 prefetch.2.10.7: 1) Downloading 'SRR2162762'... 2020-06-21T08:13:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:14:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:14:49 prefetch.2.10.7: 'SRR2162762' is valid 2020-06-21T08:14:49 prefetch.2.10.7: 1) 'SRR2162762' was downloaded successfully 2020-06-21T08:15:40 prefetch.2.10.7: 'SRR2162762' has 10 unresolved dependencies 2020-06-21T08:15:40 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T08:15:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:15:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:15:53 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:15:53 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T08:15:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:16:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:16:10 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:16:10 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T08:16:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:16:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:16:26 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:16:26 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T08:16:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:16:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:16:43 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:16:43 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T08:16:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:17:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:17:00 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:17:00 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T08:17:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:17:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:17:18 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:17:18 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T08:17:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:17:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:17:38 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:17:38 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T08:17:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:17:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:17:52 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:17:52 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T08:17:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:18:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:18:04 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:18:04 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T08:18:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:18:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:18:19 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 13006998 spots for SRR2162762/SRR2162762.sra Written 13006998 spots for SRR2162762/SRR2162762.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: 00:03:43 13006998 reads; of these: 13006998 (100.00%) were unpaired; of these: 444196 (3.42%) aligned 0 times 7670238 (58.97%) aligned exactly 1 time 4892564 (37.61%) aligned >1 times 96.58% overall alignment rate Time searching: 00:03:43 Overall time: 00:03:43 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] 4641958 / 12562802 = 0.3695 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 17:26:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.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 17:26:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:26:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:26:07: 1000000 INFO @ Sun, 21 Jun 2020 17:26:14: 2000000 INFO @ Sun, 21 Jun 2020 17:26:21: 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 17:26:28: 4000000 INFO @ Sun, 21 Jun 2020 17:26:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.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 17:26:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:26:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:26:36: 5000000 INFO @ Sun, 21 Jun 2020 17:26:36: 1000000 INFO @ Sun, 21 Jun 2020 17:26:44: 2000000 INFO @ Sun, 21 Jun 2020 17:26:44: 6000000 INFO @ Sun, 21 Jun 2020 17:26:51: 3000000 INFO @ Sun, 21 Jun 2020 17:26:51: 7000000 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 17:26:58: 4000000 INFO @ Sun, 21 Jun 2020 17:26:59: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:26:59: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:26:59: #1 total tags in treatment: 7920844 INFO @ Sun, 21 Jun 2020 17:26:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:26:59: #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 17:26:59: #1 tags after filtering in treatment: 7920766 INFO @ Sun, 21 Jun 2020 17:26:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:26:59: #1 finished! INFO @ Sun, 21 Jun 2020 17:26:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:26:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:26:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.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 17:26:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:26:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:27:00: #2 number of paired peaks: 1836 INFO @ Sun, 21 Jun 2020 17:27:00: start model_add_line... INFO @ Sun, 21 Jun 2020 17:27:00: start X-correlation... INFO @ Sun, 21 Jun 2020 17:27:00: end of X-cor INFO @ Sun, 21 Jun 2020 17:27:00: #2 finished! INFO @ Sun, 21 Jun 2020 17:27:00: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 17:27:00: #2 alternative fragment length(s) may be 3,54 bps INFO @ Sun, 21 Jun 2020 17:27:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.05_model.r WARNING @ Sun, 21 Jun 2020 17:27:00: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:27:00: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Sun, 21 Jun 2020 17:27:00: #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 17:27:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:27:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:27:05: 5000000 INFO @ Sun, 21 Jun 2020 17:27:07: 1000000 INFO @ Sun, 21 Jun 2020 17:27:13: 6000000 INFO @ Sun, 21 Jun 2020 17:27:14: 2000000 INFO @ Sun, 21 Jun 2020 17:27:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:27:20: 7000000 INFO @ Sun, 21 Jun 2020 17:27:21: 3000000 INFO @ Sun, 21 Jun 2020 17:27:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:27:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:27:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.05_summits.bed INFO @ Sun, 21 Jun 2020 17:27:26: Done! INFO @ Sun, 21 Jun 2020 17:27:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:27:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:27:26: #1 total tags in treatment: 7920844 INFO @ Sun, 21 Jun 2020 17:27:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:27:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (703 chroms): 1 millis pass2 - checking and writing primary data (2927 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:27:27: #1 tags after filtering in treatment: 7920766 INFO @ Sun, 21 Jun 2020 17:27:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:27:27: #1 finished! INFO @ Sun, 21 Jun 2020 17:27:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:27:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:27:27: #2 number of paired peaks: 1836 INFO @ Sun, 21 Jun 2020 17:27:27: start model_add_line... INFO @ Sun, 21 Jun 2020 17:27:27: start X-correlation... INFO @ Sun, 21 Jun 2020 17:27:27: end of X-cor INFO @ Sun, 21 Jun 2020 17:27:27: #2 finished! INFO @ Sun, 21 Jun 2020 17:27:27: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 17:27:27: #2 alternative fragment length(s) may be 3,54 bps INFO @ Sun, 21 Jun 2020 17:27:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.10_model.r WARNING @ Sun, 21 Jun 2020 17:27:27: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:27:27: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Sun, 21 Jun 2020 17:27:27: #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 17:27:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:27:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:27:28: 4000000 INFO @ Sun, 21 Jun 2020 17:27:34: 5000000 INFO @ Sun, 21 Jun 2020 17:27:41: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:27:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:27:47: 7000000 INFO @ Sun, 21 Jun 2020 17:27:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:27:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:27:53: #1 total tags in treatment: 7920844 INFO @ Sun, 21 Jun 2020 17:27:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:27:53: #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 17:27:53: #1 tags after filtering in treatment: 7920766 INFO @ Sun, 21 Jun 2020 17:27:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:27:53: #1 finished! INFO @ Sun, 21 Jun 2020 17:27:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:27:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:27:54: #2 number of paired peaks: 1836 INFO @ Sun, 21 Jun 2020 17:27:54: start model_add_line... INFO @ Sun, 21 Jun 2020 17:27:54: start X-correlation... INFO @ Sun, 21 Jun 2020 17:27:54: end of X-cor INFO @ Sun, 21 Jun 2020 17:27:54: #2 finished! INFO @ Sun, 21 Jun 2020 17:27:54: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 17:27:54: #2 alternative fragment length(s) may be 3,54 bps INFO @ Sun, 21 Jun 2020 17:27:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.20_model.r WARNING @ Sun, 21 Jun 2020 17:27:54: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:27:54: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Sun, 21 Jun 2020 17:27:54: #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 17:27:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:27:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:27:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:27:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:27:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.10_summits.bed INFO @ Sun, 21 Jun 2020 17:27:55: Done! pass1 - making usageList (579 chroms): 1 millis pass2 - checking and writing primary data (2238 records, 4 fields): 19 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:28:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:28:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:28:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:28:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1149359/SRX1149359.20_summits.bed INFO @ Sun, 21 Jun 2020 17:28:21: Done! pass1 - making usageList (431 chroms): 1 millis pass2 - checking and writing primary data (994 records, 4 fields): 14 millis CompletedMACS2peakCalling