Job ID = 6459794 SRX = SRX858995 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:42:47 prefetch.2.10.7: 1) Downloading 'SRR1779551'... 2020-06-21T13:42:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:43:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:43:58 prefetch.2.10.7: 'SRR1779551' is valid 2020-06-21T13:43:58 prefetch.2.10.7: 1) 'SRR1779551' was downloaded successfully 2020-06-21T13:44:50 prefetch.2.10.7: 'SRR1779551' has 10 unresolved dependencies 2020-06-21T13:44:50 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.4?vdb-ctx=refseq'... 2020-06-21T13:44:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:45:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:45:07 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:45:07 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.5?vdb-ctx=refseq'... 2020-06-21T13:45:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:45:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:45:30 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:45:30 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.3?vdb-ctx=refseq'... 2020-06-21T13:45:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:45:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:45:43 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:45:43 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.4?vdb-ctx=refseq'... 2020-06-21T13:45:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:46:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:46:01 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:46:01 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.2?vdb-ctx=refseq'... 2020-06-21T13:46:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:46:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:46:19 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:46:19 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.4?vdb-ctx=refseq'... 2020-06-21T13:46:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:46:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:46:36 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:46:36 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CM000457.1?vdb-ctx=refseq'... 2020-06-21T13:46:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:46:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:46:49 prefetch.2.10.7: 8) 'ncbi-acc:CM000457.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:46:49 prefetch.2.10.7: 9) Downloading 'ncbi-acc:CM000458.1?vdb-ctx=refseq'... 2020-06-21T13:46:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:47:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:47:02 prefetch.2.10.7: 9) 'ncbi-acc:CM000458.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:47:02 prefetch.2.10.7: 10) Downloading 'ncbi-acc:CM000459.1?vdb-ctx=refseq'... 2020-06-21T13:47:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:47:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:47:16 prefetch.2.10.7: 10) 'ncbi-acc:CM000459.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:47:16 prefetch.2.10.7: 11) Downloading 'ncbi-acc:FA000001.1?vdb-ctx=refseq'... 2020-06-21T13:47:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:47:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:47:30 prefetch.2.10.7: 11) 'ncbi-acc:FA000001.1?vdb-ctx=refseq' was downloaded successfully Read 18096495 spots for SRR1779551/SRR1779551.sra Written 18096495 spots for SRR1779551/SRR1779551.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: 00:02:58 18096495 reads; of these: 18096495 (100.00%) were unpaired; of these: 99777 (0.55%) aligned 0 times 17400010 (96.15%) aligned exactly 1 time 596708 (3.30%) aligned >1 times 99.45% overall alignment rate Time searching: 00:02:58 Overall time: 00:02:58 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] 6230 / 17996718 = 0.0003 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 22:56:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.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 22:56:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:56:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:56:20: 1000000 INFO @ Sun, 21 Jun 2020 22:56:25: 2000000 INFO @ Sun, 21 Jun 2020 22:56:31: 3000000 INFO @ Sun, 21 Jun 2020 22:56:37: 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 22:56:43: 5000000 INFO @ Sun, 21 Jun 2020 22:56:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.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 22:56:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:56:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:56:49: 6000000 INFO @ Sun, 21 Jun 2020 22:56:52: 1000000 INFO @ Sun, 21 Jun 2020 22:56:56: 7000000 INFO @ Sun, 21 Jun 2020 22:57:00: 2000000 INFO @ Sun, 21 Jun 2020 22:57:03: 8000000 INFO @ Sun, 21 Jun 2020 22:57:07: 3000000 INFO @ Sun, 21 Jun 2020 22:57:10: 9000000 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 22:57:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.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 22:57:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:57:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:57:15: 4000000 INFO @ Sun, 21 Jun 2020 22:57:17: 10000000 INFO @ Sun, 21 Jun 2020 22:57:21: 1000000 INFO @ Sun, 21 Jun 2020 22:57:23: 5000000 INFO @ Sun, 21 Jun 2020 22:57:25: 11000000 INFO @ Sun, 21 Jun 2020 22:57:28: 2000000 INFO @ Sun, 21 Jun 2020 22:57:31: 6000000 INFO @ Sun, 21 Jun 2020 22:57:32: 12000000 INFO @ Sun, 21 Jun 2020 22:57:36: 3000000 INFO @ Sun, 21 Jun 2020 22:57:39: 7000000 INFO @ Sun, 21 Jun 2020 22:57:39: 13000000 INFO @ Sun, 21 Jun 2020 22:57:43: 4000000 INFO @ Sun, 21 Jun 2020 22:57:47: 8000000 INFO @ Sun, 21 Jun 2020 22:57:47: 14000000 INFO @ Sun, 21 Jun 2020 22:57:51: 5000000 INFO @ Sun, 21 Jun 2020 22:57:55: 15000000 INFO @ Sun, 21 Jun 2020 22:57:55: 9000000 INFO @ Sun, 21 Jun 2020 22:57:58: 6000000 INFO @ Sun, 21 Jun 2020 22:58:03: 16000000 INFO @ Sun, 21 Jun 2020 22:58:03: 10000000 INFO @ Sun, 21 Jun 2020 22:58:06: 7000000 INFO @ Sun, 21 Jun 2020 22:58:10: 17000000 INFO @ Sun, 21 Jun 2020 22:58:11: 11000000 INFO @ Sun, 21 Jun 2020 22:58:14: 8000000 INFO @ Sun, 21 Jun 2020 22:58:18: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:58:18: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:58:18: #1 total tags in treatment: 17990488 INFO @ Sun, 21 Jun 2020 22:58:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:58:18: #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 22:58:19: #1 tags after filtering in treatment: 17990286 INFO @ Sun, 21 Jun 2020 22:58:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:58:19: #1 finished! INFO @ Sun, 21 Jun 2020 22:58:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:58:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:58:20: 12000000 INFO @ Sun, 21 Jun 2020 22:58:20: #2 number of paired peaks: 3460 INFO @ Sun, 21 Jun 2020 22:58:20: start model_add_line... INFO @ Sun, 21 Jun 2020 22:58:21: start X-correlation... INFO @ Sun, 21 Jun 2020 22:58:21: end of X-cor INFO @ Sun, 21 Jun 2020 22:58:21: #2 finished! INFO @ Sun, 21 Jun 2020 22:58:21: #2 predicted fragment length is 90 bps INFO @ Sun, 21 Jun 2020 22:58:21: #2 alternative fragment length(s) may be 90 bps INFO @ Sun, 21 Jun 2020 22:58:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.05_model.r WARNING @ Sun, 21 Jun 2020 22:58:21: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:58:21: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sun, 21 Jun 2020 22:58:21: #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 22:58:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:58:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:58:21: 9000000 INFO @ Sun, 21 Jun 2020 22:58:28: 13000000 INFO @ Sun, 21 Jun 2020 22:58:29: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:58:36: 11000000 INFO @ Sun, 21 Jun 2020 22:58:37: 14000000 INFO @ Sun, 21 Jun 2020 22:58:44: 12000000 INFO @ Sun, 21 Jun 2020 22:58:45: 15000000 INFO @ Sun, 21 Jun 2020 22:58:51: 13000000 INFO @ Sun, 21 Jun 2020 22:58:53: 16000000 INFO @ Sun, 21 Jun 2020 22:58:58: 14000000 INFO @ Sun, 21 Jun 2020 22:59:00: 17000000 INFO @ Sun, 21 Jun 2020 22:59:05: 15000000 INFO @ Sun, 21 Jun 2020 22:59:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:59:08: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:59:08: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:59:08: #1 total tags in treatment: 17990488 INFO @ Sun, 21 Jun 2020 22:59:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:59:08: #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 22:59:08: #1 tags after filtering in treatment: 17990286 INFO @ Sun, 21 Jun 2020 22:59:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:59:08: #1 finished! INFO @ Sun, 21 Jun 2020 22:59:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:59:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:59:10: #2 number of paired peaks: 3460 INFO @ Sun, 21 Jun 2020 22:59:10: start model_add_line... INFO @ Sun, 21 Jun 2020 22:59:10: start X-correlation... INFO @ Sun, 21 Jun 2020 22:59:10: end of X-cor INFO @ Sun, 21 Jun 2020 22:59:10: #2 finished! INFO @ Sun, 21 Jun 2020 22:59:10: #2 predicted fragment length is 90 bps INFO @ Sun, 21 Jun 2020 22:59:10: #2 alternative fragment length(s) may be 90 bps INFO @ Sun, 21 Jun 2020 22:59:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.10_model.r WARNING @ Sun, 21 Jun 2020 22:59:10: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:59:10: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sun, 21 Jun 2020 22:59:10: #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 22:59:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:59:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:59:12: 16000000 INFO @ Sun, 21 Jun 2020 22:59:18: 17000000 INFO @ Sun, 21 Jun 2020 22:59:25: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:59:25: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:59:25: #1 total tags in treatment: 17990488 INFO @ Sun, 21 Jun 2020 22:59:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:59:25: #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 22:59:25: #1 tags after filtering in treatment: 17990286 INFO @ Sun, 21 Jun 2020 22:59:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:59:25: #1 finished! INFO @ Sun, 21 Jun 2020 22:59:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:59:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:59:27: #2 number of paired peaks: 3460 INFO @ Sun, 21 Jun 2020 22:59:27: start model_add_line... INFO @ Sun, 21 Jun 2020 22:59:27: start X-correlation... INFO @ Sun, 21 Jun 2020 22:59:27: end of X-cor INFO @ Sun, 21 Jun 2020 22:59:27: #2 finished! INFO @ Sun, 21 Jun 2020 22:59:27: #2 predicted fragment length is 90 bps INFO @ Sun, 21 Jun 2020 22:59:27: #2 alternative fragment length(s) may be 90 bps INFO @ Sun, 21 Jun 2020 22:59:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.20_model.r WARNING @ Sun, 21 Jun 2020 22:59:27: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:59:27: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sun, 21 Jun 2020 22:59:27: #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 22:59:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:59:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:59:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:59:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:59:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.05_summits.bed INFO @ Sun, 21 Jun 2020 22:59:28: Done! pass1 - making usageList (46 chroms): 2 millis pass2 - checking and writing primary data (14864 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:59:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:00:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:00:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.10_peaks.xls INFO @ Sun, 21 Jun 2020 23:00:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:00:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.10_summits.bed INFO @ Sun, 21 Jun 2020 23:00:17: Done! pass1 - making usageList (33 chroms): 2 millis pass2 - checking and writing primary data (10929 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:00:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.20_peaks.xls INFO @ Sun, 21 Jun 2020 23:00:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:00:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX858995/SRX858995.20_summits.bed INFO @ Sun, 21 Jun 2020 23:00:29: Done! pass1 - making usageList (24 chroms): 1 millis pass2 - checking and writing primary data (6844 records, 4 fields): 8 millis CompletedMACS2peakCalling