Job ID = 6527612 SRX = SRX1433361 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:51:38 prefetch.2.10.7: 1) Downloading 'SRR2919826'... 2020-06-29T12:51:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:55:27 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:55:27 prefetch.2.10.7: 1) 'SRR2919826' was downloaded successfully Read 43337377 spots for SRR2919826/SRR2919826.sra Written 43337377 spots for SRR2919826/SRR2919826.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: 00:21:55 43337377 reads; of these: 43337377 (100.00%) were unpaired; of these: 1580737 (3.65%) aligned 0 times 21908101 (50.55%) aligned exactly 1 time 19848539 (45.80%) aligned >1 times 96.35% overall alignment rate Time searching: 00:21:55 Overall time: 00:21:55 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 20457169 / 41756640 = 0.4899 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 @ Mon, 29 Jun 2020 22:41:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.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 @ Mon, 29 Jun 2020 22:41:07: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:41:07: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:41:12: 1000000 INFO @ Mon, 29 Jun 2020 22:41:17: 2000000 INFO @ Mon, 29 Jun 2020 22:41:23: 3000000 INFO @ Mon, 29 Jun 2020 22:41:28: 4000000 INFO @ Mon, 29 Jun 2020 22:41:33: 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 @ Mon, 29 Jun 2020 22:41:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.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 @ Mon, 29 Jun 2020 22:41:36: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:41:36: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:41:39: 6000000 INFO @ Mon, 29 Jun 2020 22:41:42: 1000000 INFO @ Mon, 29 Jun 2020 22:41:44: 7000000 INFO @ Mon, 29 Jun 2020 22:41:48: 2000000 INFO @ Mon, 29 Jun 2020 22:41:50: 8000000 INFO @ Mon, 29 Jun 2020 22:41:55: 3000000 INFO @ Mon, 29 Jun 2020 22:41:55: 9000000 INFO @ Mon, 29 Jun 2020 22:42:01: 4000000 INFO @ Mon, 29 Jun 2020 22:42:02: 10000000 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 @ Mon, 29 Jun 2020 22:42:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.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 @ Mon, 29 Jun 2020 22:42:07: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:42:07: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:42:07: 5000000 INFO @ Mon, 29 Jun 2020 22:42:07: 11000000 INFO @ Mon, 29 Jun 2020 22:42:13: 12000000 INFO @ Mon, 29 Jun 2020 22:42:13: 1000000 INFO @ Mon, 29 Jun 2020 22:42:14: 6000000 INFO @ Mon, 29 Jun 2020 22:42:19: 13000000 INFO @ Mon, 29 Jun 2020 22:42:20: 2000000 INFO @ Mon, 29 Jun 2020 22:42:21: 7000000 INFO @ Mon, 29 Jun 2020 22:42:24: 14000000 INFO @ Mon, 29 Jun 2020 22:42:27: 3000000 INFO @ Mon, 29 Jun 2020 22:42:28: 8000000 INFO @ Mon, 29 Jun 2020 22:42:30: 15000000 INFO @ Mon, 29 Jun 2020 22:42:34: 4000000 INFO @ Mon, 29 Jun 2020 22:42:34: 9000000 INFO @ Mon, 29 Jun 2020 22:42:36: 16000000 INFO @ Mon, 29 Jun 2020 22:42:41: 5000000 INFO @ Mon, 29 Jun 2020 22:42:42: 17000000 INFO @ Mon, 29 Jun 2020 22:42:42: 10000000 INFO @ Mon, 29 Jun 2020 22:42:47: 6000000 INFO @ Mon, 29 Jun 2020 22:42:48: 18000000 INFO @ Mon, 29 Jun 2020 22:42:49: 11000000 INFO @ Mon, 29 Jun 2020 22:42:54: 19000000 INFO @ Mon, 29 Jun 2020 22:42:54: 7000000 INFO @ Mon, 29 Jun 2020 22:42:57: 12000000 INFO @ Mon, 29 Jun 2020 22:43:00: 20000000 INFO @ Mon, 29 Jun 2020 22:43:00: 8000000 INFO @ Mon, 29 Jun 2020 22:43:04: 13000000 INFO @ Mon, 29 Jun 2020 22:43:06: 21000000 INFO @ Mon, 29 Jun 2020 22:43:06: 9000000 INFO @ Mon, 29 Jun 2020 22:43:08: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:43:08: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:43:08: #1 total tags in treatment: 21299471 INFO @ Mon, 29 Jun 2020 22:43:08: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:43:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:43:08: #1 tags after filtering in treatment: 21299471 INFO @ Mon, 29 Jun 2020 22:43:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:43:08: #1 finished! INFO @ Mon, 29 Jun 2020 22:43:08: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:43:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:43:10: #2 number of paired peaks: 1679 INFO @ Mon, 29 Jun 2020 22:43:10: start model_add_line... INFO @ Mon, 29 Jun 2020 22:43:10: start X-correlation... INFO @ Mon, 29 Jun 2020 22:43:10: end of X-cor INFO @ Mon, 29 Jun 2020 22:43:10: #2 finished! INFO @ Mon, 29 Jun 2020 22:43:10: #2 predicted fragment length is 67 bps INFO @ Mon, 29 Jun 2020 22:43:10: #2 alternative fragment length(s) may be 2,67,541 bps INFO @ Mon, 29 Jun 2020 22:43:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.05_model.r WARNING @ Mon, 29 Jun 2020 22:43:10: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:43:10: #2 You may need to consider one of the other alternative d(s): 2,67,541 WARNING @ Mon, 29 Jun 2020 22:43:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:43:10: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:43:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:43:11: 14000000 INFO @ Mon, 29 Jun 2020 22:43:13: 10000000 INFO @ Mon, 29 Jun 2020 22:43:18: 15000000 INFO @ Mon, 29 Jun 2020 22:43:19: 11000000 INFO @ Mon, 29 Jun 2020 22:43:24: 16000000 INFO @ Mon, 29 Jun 2020 22:43:25: 12000000 INFO @ Mon, 29 Jun 2020 22:43:29: 17000000 INFO @ Mon, 29 Jun 2020 22:43:32: 13000000 INFO @ Mon, 29 Jun 2020 22:43:35: 18000000 INFO @ Mon, 29 Jun 2020 22:43:38: 14000000 INFO @ Mon, 29 Jun 2020 22:43:41: 19000000 INFO @ Mon, 29 Jun 2020 22:43:44: 15000000 INFO @ Mon, 29 Jun 2020 22:43:47: 20000000 INFO @ Mon, 29 Jun 2020 22:43:50: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:43:51: 16000000 INFO @ Mon, 29 Jun 2020 22:43:53: 21000000 INFO @ Mon, 29 Jun 2020 22:43:54: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:43:54: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:43:54: #1 total tags in treatment: 21299471 INFO @ Mon, 29 Jun 2020 22:43:54: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:43:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:43:55: #1 tags after filtering in treatment: 21299471 INFO @ Mon, 29 Jun 2020 22:43:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:43:55: #1 finished! INFO @ Mon, 29 Jun 2020 22:43:55: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:43:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:43:56: #2 number of paired peaks: 1679 INFO @ Mon, 29 Jun 2020 22:43:56: start model_add_line... INFO @ Mon, 29 Jun 2020 22:43:57: start X-correlation... INFO @ Mon, 29 Jun 2020 22:43:57: 17000000 INFO @ Mon, 29 Jun 2020 22:43:57: end of X-cor INFO @ Mon, 29 Jun 2020 22:43:57: #2 finished! INFO @ Mon, 29 Jun 2020 22:43:57: #2 predicted fragment length is 67 bps INFO @ Mon, 29 Jun 2020 22:43:57: #2 alternative fragment length(s) may be 2,67,541 bps INFO @ Mon, 29 Jun 2020 22:43:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.10_model.r WARNING @ Mon, 29 Jun 2020 22:43:57: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:43:57: #2 You may need to consider one of the other alternative d(s): 2,67,541 WARNING @ Mon, 29 Jun 2020 22:43:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:43:57: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:43:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:44:03: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:44:09: 19000000 INFO @ Mon, 29 Jun 2020 22:44:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:44:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:44:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.05_summits.bed INFO @ Mon, 29 Jun 2020 22:44:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5635 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:44:15: 20000000 INFO @ Mon, 29 Jun 2020 22:44:21: 21000000 INFO @ Mon, 29 Jun 2020 22:44:23: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:44:23: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:44:23: #1 total tags in treatment: 21299471 INFO @ Mon, 29 Jun 2020 22:44:23: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:44:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:44:24: #1 tags after filtering in treatment: 21299471 INFO @ Mon, 29 Jun 2020 22:44:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:44:24: #1 finished! INFO @ Mon, 29 Jun 2020 22:44:24: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:44:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:44:25: #2 number of paired peaks: 1679 INFO @ Mon, 29 Jun 2020 22:44:25: start model_add_line... INFO @ Mon, 29 Jun 2020 22:44:25: start X-correlation... INFO @ Mon, 29 Jun 2020 22:44:25: end of X-cor INFO @ Mon, 29 Jun 2020 22:44:25: #2 finished! INFO @ Mon, 29 Jun 2020 22:44:25: #2 predicted fragment length is 67 bps INFO @ Mon, 29 Jun 2020 22:44:25: #2 alternative fragment length(s) may be 2,67,541 bps INFO @ Mon, 29 Jun 2020 22:44:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.20_model.r WARNING @ Mon, 29 Jun 2020 22:44:25: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:44:25: #2 You may need to consider one of the other alternative d(s): 2,67,541 WARNING @ Mon, 29 Jun 2020 22:44:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:44:25: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:44:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:44:36: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:44:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:44:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:44:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.10_summits.bed INFO @ Mon, 29 Jun 2020 22:44:55: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3042 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:45:05: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:45:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:45:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:45:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1433361/SRX1433361.20_summits.bed INFO @ Mon, 29 Jun 2020 22:45:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1934 records, 4 fields): 4 millis CompletedMACS2peakCalling