Job ID = 6454249 SRX = SRX193325 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:57:04 prefetch.2.10.7: 1) Downloading 'SRR585058'... 2020-06-21T08:57:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:00:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:00:14 prefetch.2.10.7: 1) 'SRR585058' was downloaded successfully Read 26260919 spots for SRR585058/SRR585058.sra Written 26260919 spots for SRR585058/SRR585058.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: 00:07:13 26260919 reads; of these: 26260919 (100.00%) were unpaired; of these: 1123451 (4.28%) aligned 0 times 17542096 (66.80%) aligned exactly 1 time 7595372 (28.92%) aligned >1 times 95.72% overall alignment rate Time searching: 00:07:13 Overall time: 00:07:13 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 12 files... [bam_rmdupse_core] 3592925 / 25137468 = 0.1429 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 18:15:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.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 18:15:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:15:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:15:05: 1000000 INFO @ Sun, 21 Jun 2020 18:15:11: 2000000 INFO @ Sun, 21 Jun 2020 18:15:16: 3000000 INFO @ Sun, 21 Jun 2020 18:15:22: 4000000 INFO @ Sun, 21 Jun 2020 18:15:28: 5000000 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 18:15:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.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 18:15:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:15:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:15:34: 6000000 INFO @ Sun, 21 Jun 2020 18:15:36: 1000000 INFO @ Sun, 21 Jun 2020 18:15:40: 7000000 INFO @ Sun, 21 Jun 2020 18:15:42: 2000000 INFO @ Sun, 21 Jun 2020 18:15:46: 8000000 INFO @ Sun, 21 Jun 2020 18:15:48: 3000000 INFO @ Sun, 21 Jun 2020 18:15:52: 9000000 INFO @ Sun, 21 Jun 2020 18:15:55: 4000000 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 18:15:59: 10000000 INFO @ Sun, 21 Jun 2020 18:16:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.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 18:16:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:16:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:16:01: 5000000 INFO @ Sun, 21 Jun 2020 18:16:05: 11000000 INFO @ Sun, 21 Jun 2020 18:16:06: 1000000 INFO @ Sun, 21 Jun 2020 18:16:07: 6000000 INFO @ Sun, 21 Jun 2020 18:16:11: 12000000 INFO @ Sun, 21 Jun 2020 18:16:12: 2000000 INFO @ Sun, 21 Jun 2020 18:16:14: 7000000 INFO @ Sun, 21 Jun 2020 18:16:18: 13000000 INFO @ Sun, 21 Jun 2020 18:16:19: 3000000 INFO @ Sun, 21 Jun 2020 18:16:20: 8000000 INFO @ Sun, 21 Jun 2020 18:16:24: 14000000 INFO @ Sun, 21 Jun 2020 18:16:25: 4000000 INFO @ Sun, 21 Jun 2020 18:16:26: 9000000 INFO @ Sun, 21 Jun 2020 18:16:30: 15000000 INFO @ Sun, 21 Jun 2020 18:16:32: 5000000 INFO @ Sun, 21 Jun 2020 18:16:33: 10000000 INFO @ Sun, 21 Jun 2020 18:16:37: 16000000 INFO @ Sun, 21 Jun 2020 18:16:38: 6000000 INFO @ Sun, 21 Jun 2020 18:16:39: 11000000 INFO @ Sun, 21 Jun 2020 18:16:43: 17000000 INFO @ Sun, 21 Jun 2020 18:16:45: 7000000 INFO @ Sun, 21 Jun 2020 18:16:46: 12000000 INFO @ Sun, 21 Jun 2020 18:16:50: 18000000 INFO @ Sun, 21 Jun 2020 18:16:51: 8000000 INFO @ Sun, 21 Jun 2020 18:16:52: 13000000 INFO @ Sun, 21 Jun 2020 18:16:56: 19000000 INFO @ Sun, 21 Jun 2020 18:16:57: 9000000 INFO @ Sun, 21 Jun 2020 18:16:59: 14000000 INFO @ Sun, 21 Jun 2020 18:17:03: 20000000 INFO @ Sun, 21 Jun 2020 18:17:04: 10000000 INFO @ Sun, 21 Jun 2020 18:17:05: 15000000 INFO @ Sun, 21 Jun 2020 18:17:09: 21000000 INFO @ Sun, 21 Jun 2020 18:17:10: 11000000 INFO @ Sun, 21 Jun 2020 18:17:11: 16000000 INFO @ Sun, 21 Jun 2020 18:17:13: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:17:13: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:17:13: #1 total tags in treatment: 21544543 INFO @ Sun, 21 Jun 2020 18:17:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:17:13: #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 18:17:13: #1 tags after filtering in treatment: 21544475 INFO @ Sun, 21 Jun 2020 18:17:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:17:13: #1 finished! INFO @ Sun, 21 Jun 2020 18:17:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:17:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:17:15: #2 number of paired peaks: 1015 INFO @ Sun, 21 Jun 2020 18:17:15: start model_add_line... INFO @ Sun, 21 Jun 2020 18:17:15: start X-correlation... INFO @ Sun, 21 Jun 2020 18:17:15: end of X-cor INFO @ Sun, 21 Jun 2020 18:17:15: #2 finished! INFO @ Sun, 21 Jun 2020 18:17:15: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 18:17:15: #2 alternative fragment length(s) may be 1,44 bps INFO @ Sun, 21 Jun 2020 18:17:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.05_model.r WARNING @ Sun, 21 Jun 2020 18:17:15: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:17:15: #2 You may need to consider one of the other alternative d(s): 1,44 WARNING @ Sun, 21 Jun 2020 18:17:15: #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 18:17:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:17:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:17:17: 12000000 INFO @ Sun, 21 Jun 2020 18:17:18: 17000000 INFO @ Sun, 21 Jun 2020 18:17:23: 13000000 INFO @ Sun, 21 Jun 2020 18:17:24: 18000000 INFO @ Sun, 21 Jun 2020 18:17:30: 14000000 INFO @ Sun, 21 Jun 2020 18:17:31: 19000000 INFO @ Sun, 21 Jun 2020 18:17:36: 15000000 INFO @ Sun, 21 Jun 2020 18:17:37: 20000000 INFO @ Sun, 21 Jun 2020 18:17:44: 16000000 INFO @ Sun, 21 Jun 2020 18:17:44: 21000000 INFO @ Sun, 21 Jun 2020 18:17:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:17:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:17:48: #1 total tags in treatment: 21544543 INFO @ Sun, 21 Jun 2020 18:17:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:17:48: #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 18:17:48: #1 tags after filtering in treatment: 21544475 INFO @ Sun, 21 Jun 2020 18:17:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:17:48: #1 finished! INFO @ Sun, 21 Jun 2020 18:17:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:17:48: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:17:50: #2 number of paired peaks: 1015 INFO @ Sun, 21 Jun 2020 18:17:50: start model_add_line... INFO @ Sun, 21 Jun 2020 18:17:50: start X-correlation... INFO @ Sun, 21 Jun 2020 18:17:50: end of X-cor INFO @ Sun, 21 Jun 2020 18:17:50: #2 finished! INFO @ Sun, 21 Jun 2020 18:17:50: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 18:17:50: #2 alternative fragment length(s) may be 1,44 bps INFO @ Sun, 21 Jun 2020 18:17:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.10_model.r WARNING @ Sun, 21 Jun 2020 18:17:50: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:17:50: #2 You may need to consider one of the other alternative d(s): 1,44 WARNING @ Sun, 21 Jun 2020 18:17:50: #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 18:17:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:17:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:17:50: 17000000 INFO @ Sun, 21 Jun 2020 18:17:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:17:57: 18000000 INFO @ Sun, 21 Jun 2020 18:18:03: 19000000 INFO @ Sun, 21 Jun 2020 18:18:08: 20000000 INFO @ Sun, 21 Jun 2020 18:18:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:18:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:18:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.05_summits.bed INFO @ Sun, 21 Jun 2020 18:18:14: Done! INFO @ Sun, 21 Jun 2020 18:18:14: 21000000 pass1 - making usageList (644 chroms): 1 millis pass2 - checking and writing primary data (2970 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:18:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:18:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:18:17: #1 total tags in treatment: 21544543 INFO @ Sun, 21 Jun 2020 18:18:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:18:17: #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 18:18:18: #1 tags after filtering in treatment: 21544475 INFO @ Sun, 21 Jun 2020 18:18:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:18:18: #1 finished! INFO @ Sun, 21 Jun 2020 18:18:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:18:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:18:19: #2 number of paired peaks: 1015 INFO @ Sun, 21 Jun 2020 18:18:19: start model_add_line... INFO @ Sun, 21 Jun 2020 18:18:19: start X-correlation... INFO @ Sun, 21 Jun 2020 18:18:19: end of X-cor INFO @ Sun, 21 Jun 2020 18:18:19: #2 finished! INFO @ Sun, 21 Jun 2020 18:18:19: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 18:18:19: #2 alternative fragment length(s) may be 1,44 bps INFO @ Sun, 21 Jun 2020 18:18:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.20_model.r WARNING @ Sun, 21 Jun 2020 18:18:19: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:18:19: #2 You may need to consider one of the other alternative d(s): 1,44 WARNING @ Sun, 21 Jun 2020 18:18:19: #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 18:18:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:18:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:18:29: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:18:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:18:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:18:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.10_summits.bed INFO @ Sun, 21 Jun 2020 18:18:48: Done! pass1 - making usageList (546 chroms): 2 millis pass2 - checking and writing primary data (2318 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:18:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:19:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:19:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:19:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193325/SRX193325.20_summits.bed INFO @ Sun, 21 Jun 2020 18:19:18: Done! pass1 - making usageList (404 chroms): 1 millis pass2 - checking and writing primary data (1114 records, 4 fields): 12 millis CompletedMACS2peakCalling