Job ID = 6457031 SRX = SRX4315053 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:21:54 prefetch.2.10.7: 1) Downloading 'SRR7444514'... 2020-06-21T11:21:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:22:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:22:56 prefetch.2.10.7: 'SRR7444514' is valid 2020-06-21T11:22:56 prefetch.2.10.7: 1) 'SRR7444514' was downloaded successfully 2020-06-21T11:23:33 prefetch.2.10.7: 'SRR7444514' has 7 unresolved dependencies 2020-06-21T11:23:33 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.5?vdb-ctx=refseq'... 2020-06-21T11:23:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:23:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:23:52 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:23:52 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.6?vdb-ctx=refseq'... 2020-06-21T11:23:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:24:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:24:11 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.6?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:24:11 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.4?vdb-ctx=refseq'... 2020-06-21T11:24:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:24:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:24:23 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:24:23 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.5?vdb-ctx=refseq'... 2020-06-21T11:24:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:24:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:24:42 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:24:42 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.3?vdb-ctx=refseq'... 2020-06-21T11:24:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:25:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:25:02 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:25:02 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.5?vdb-ctx=refseq'... 2020-06-21T11:25:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:25:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:25:18 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:25:18 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CP007106.1?vdb-ctx=refseq'... 2020-06-21T11:25:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:25:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:25:33 prefetch.2.10.7: 8) 'ncbi-acc:CP007106.1?vdb-ctx=refseq' was downloaded successfully Read 9002283 spots for SRR7444514/SRR7444514.sra Written 9002283 spots for SRR7444514/SRR7444514.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: 00:02:20 9002283 reads; of these: 9002283 (100.00%) were unpaired; of these: 2741 (0.03%) aligned 0 times 8118189 (90.18%) aligned exactly 1 time 881353 (9.79%) aligned >1 times 99.97% overall alignment rate Time searching: 00:02:20 Overall time: 00:02:20 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_rmdupse_core] 3560535 / 8999542 = 0.3956 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 20:31:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.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 20:31:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:31:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:31:13: 1000000 INFO @ Sun, 21 Jun 2020 20:31:20: 2000000 INFO @ Sun, 21 Jun 2020 20:31:28: 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 20:31:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.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 20:31:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:31:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:31:36: 4000000 INFO @ Sun, 21 Jun 2020 20:31:43: 1000000 INFO @ Sun, 21 Jun 2020 20:31:44: 5000000 INFO @ Sun, 21 Jun 2020 20:31:48: #1 tag size is determined as 73 bps INFO @ Sun, 21 Jun 2020 20:31:48: #1 tag size = 73 INFO @ Sun, 21 Jun 2020 20:31:48: #1 total tags in treatment: 5439007 INFO @ Sun, 21 Jun 2020 20:31:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:31:48: #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 20:31:48: #1 tags after filtering in treatment: 5438786 INFO @ Sun, 21 Jun 2020 20:31:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:31:48: #1 finished! INFO @ Sun, 21 Jun 2020 20:31:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:31:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:31:49: #2 number of paired peaks: 2951 INFO @ Sun, 21 Jun 2020 20:31:49: start model_add_line... INFO @ Sun, 21 Jun 2020 20:31:49: start X-correlation... INFO @ Sun, 21 Jun 2020 20:31:49: end of X-cor INFO @ Sun, 21 Jun 2020 20:31:49: #2 finished! INFO @ Sun, 21 Jun 2020 20:31:49: #2 predicted fragment length is 103 bps INFO @ Sun, 21 Jun 2020 20:31:49: #2 alternative fragment length(s) may be 103 bps INFO @ Sun, 21 Jun 2020 20:31:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.05_model.r WARNING @ Sun, 21 Jun 2020 20:31:49: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:31:49: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Sun, 21 Jun 2020 20:31:49: #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 20:31:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:31:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:31:51: 2000000 INFO @ Sun, 21 Jun 2020 20:31:58: 3000000 INFO @ Sun, 21 Jun 2020 20:32:03: #3 Call peaks for each chromosome... 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 20:32:04: 4000000 INFO @ Sun, 21 Jun 2020 20:32:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.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 20:32:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:32:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:32:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:32:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:32:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.05_summits.bed INFO @ Sun, 21 Jun 2020 20:32:10: Done! pass1 - making usageList (87 chroms): 1 millis pass2 - checking and writing primary data (5956 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:32:12: 5000000 INFO @ Sun, 21 Jun 2020 20:32:13: 1000000 INFO @ Sun, 21 Jun 2020 20:32:16: #1 tag size is determined as 73 bps INFO @ Sun, 21 Jun 2020 20:32:16: #1 tag size = 73 INFO @ Sun, 21 Jun 2020 20:32:16: #1 total tags in treatment: 5439007 INFO @ Sun, 21 Jun 2020 20:32:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:32:16: #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 20:32:16: #1 tags after filtering in treatment: 5438786 INFO @ Sun, 21 Jun 2020 20:32:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:32:16: #1 finished! INFO @ Sun, 21 Jun 2020 20:32:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:32:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:32:17: #2 number of paired peaks: 2951 INFO @ Sun, 21 Jun 2020 20:32:17: start model_add_line... INFO @ Sun, 21 Jun 2020 20:32:17: start X-correlation... INFO @ Sun, 21 Jun 2020 20:32:17: end of X-cor INFO @ Sun, 21 Jun 2020 20:32:17: #2 finished! INFO @ Sun, 21 Jun 2020 20:32:17: #2 predicted fragment length is 103 bps INFO @ Sun, 21 Jun 2020 20:32:17: #2 alternative fragment length(s) may be 103 bps INFO @ Sun, 21 Jun 2020 20:32:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.10_model.r WARNING @ Sun, 21 Jun 2020 20:32:17: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:32:17: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Sun, 21 Jun 2020 20:32:17: #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 20:32:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:32:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:32:21: 2000000 INFO @ Sun, 21 Jun 2020 20:32:29: 3000000 INFO @ Sun, 21 Jun 2020 20:32:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:32:36: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:32:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:32:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:32:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.10_summits.bed INFO @ Sun, 21 Jun 2020 20:32:39: Done! pass1 - making usageList (62 chroms): 2 millis pass2 - checking and writing primary data (3215 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:32:44: 5000000 INFO @ Sun, 21 Jun 2020 20:32:47: #1 tag size is determined as 73 bps INFO @ Sun, 21 Jun 2020 20:32:47: #1 tag size = 73 INFO @ Sun, 21 Jun 2020 20:32:47: #1 total tags in treatment: 5439007 INFO @ Sun, 21 Jun 2020 20:32:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:32:47: #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 20:32:48: #1 tags after filtering in treatment: 5438786 INFO @ Sun, 21 Jun 2020 20:32:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:32:48: #1 finished! INFO @ Sun, 21 Jun 2020 20:32:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:32:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:32:48: #2 number of paired peaks: 2951 INFO @ Sun, 21 Jun 2020 20:32:48: start model_add_line... INFO @ Sun, 21 Jun 2020 20:32:48: start X-correlation... INFO @ Sun, 21 Jun 2020 20:32:48: end of X-cor INFO @ Sun, 21 Jun 2020 20:32:48: #2 finished! INFO @ Sun, 21 Jun 2020 20:32:48: #2 predicted fragment length is 103 bps INFO @ Sun, 21 Jun 2020 20:32:48: #2 alternative fragment length(s) may be 103 bps INFO @ Sun, 21 Jun 2020 20:32:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.20_model.r WARNING @ Sun, 21 Jun 2020 20:32:48: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:32:48: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Sun, 21 Jun 2020 20:32:48: #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 20:32:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:32:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:33:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:33:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:33:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:33:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315053/SRX4315053.20_summits.bed INFO @ Sun, 21 Jun 2020 20:33:10: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (1475 records, 4 fields): 18 millis CompletedMACS2peakCalling