Job ID = 6528097 SRX = SRX4580644 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:31:52 prefetch.2.10.7: 1) Downloading 'SRR7724135'... 2020-06-29T14:31:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:42:23 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:42:23 prefetch.2.10.7: 1) 'SRR7724135' was downloaded successfully Read 77034656 spots for SRR7724135/SRR7724135.sra Written 77034656 spots for SRR7724135/SRR7724135.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: 00:26:19 77034656 reads; of these: 77034656 (100.00%) were unpaired; of these: 30529709 (39.63%) aligned 0 times 21778741 (28.27%) aligned exactly 1 time 24726206 (32.10%) aligned >1 times 60.37% overall alignment rate Time searching: 00:26:19 Overall time: 00:26:19 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] 13685458 / 46504947 = 0.2943 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 @ Tue, 30 Jun 2020 00:42:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.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 @ Tue, 30 Jun 2020 00:42:04: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:42:04: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:42:10: 1000000 INFO @ Tue, 30 Jun 2020 00:42:16: 2000000 INFO @ Tue, 30 Jun 2020 00:42:22: 3000000 INFO @ Tue, 30 Jun 2020 00:42:28: 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 @ Tue, 30 Jun 2020 00:42:33: 5000000 INFO @ Tue, 30 Jun 2020 00:42:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.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 @ Tue, 30 Jun 2020 00:42:34: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:42:34: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:42:40: 6000000 INFO @ Tue, 30 Jun 2020 00:42:41: 1000000 INFO @ Tue, 30 Jun 2020 00:42:46: 7000000 INFO @ Tue, 30 Jun 2020 00:42:47: 2000000 INFO @ Tue, 30 Jun 2020 00:42:52: 8000000 INFO @ Tue, 30 Jun 2020 00:42:54: 3000000 INFO @ Tue, 30 Jun 2020 00:42:59: 9000000 INFO @ Tue, 30 Jun 2020 00:43:00: 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 @ Tue, 30 Jun 2020 00:43:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.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 @ Tue, 30 Jun 2020 00:43:04: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:43:04: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:43:05: 10000000 INFO @ Tue, 30 Jun 2020 00:43:07: 5000000 INFO @ Tue, 30 Jun 2020 00:43:11: 1000000 INFO @ Tue, 30 Jun 2020 00:43:12: 11000000 INFO @ Tue, 30 Jun 2020 00:43:14: 6000000 INFO @ Tue, 30 Jun 2020 00:43:18: 12000000 INFO @ Tue, 30 Jun 2020 00:43:19: 2000000 INFO @ Tue, 30 Jun 2020 00:43:20: 7000000 INFO @ Tue, 30 Jun 2020 00:43:25: 13000000 INFO @ Tue, 30 Jun 2020 00:43:26: 3000000 INFO @ Tue, 30 Jun 2020 00:43:27: 8000000 INFO @ Tue, 30 Jun 2020 00:43:32: 14000000 INFO @ Tue, 30 Jun 2020 00:43:33: 4000000 INFO @ Tue, 30 Jun 2020 00:43:35: 9000000 INFO @ Tue, 30 Jun 2020 00:43:39: 15000000 INFO @ Tue, 30 Jun 2020 00:43:40: 5000000 INFO @ Tue, 30 Jun 2020 00:43:41: 10000000 INFO @ Tue, 30 Jun 2020 00:43:45: 16000000 INFO @ Tue, 30 Jun 2020 00:43:47: 6000000 INFO @ Tue, 30 Jun 2020 00:43:48: 11000000 INFO @ Tue, 30 Jun 2020 00:43:52: 17000000 INFO @ Tue, 30 Jun 2020 00:43:54: 7000000 INFO @ Tue, 30 Jun 2020 00:43:54: 12000000 INFO @ Tue, 30 Jun 2020 00:43:59: 18000000 INFO @ Tue, 30 Jun 2020 00:44:01: 13000000 INFO @ Tue, 30 Jun 2020 00:44:01: 8000000 INFO @ Tue, 30 Jun 2020 00:44:05: 19000000 INFO @ Tue, 30 Jun 2020 00:44:08: 14000000 INFO @ Tue, 30 Jun 2020 00:44:08: 9000000 INFO @ Tue, 30 Jun 2020 00:44:12: 20000000 INFO @ Tue, 30 Jun 2020 00:44:14: 15000000 INFO @ Tue, 30 Jun 2020 00:44:15: 10000000 INFO @ Tue, 30 Jun 2020 00:44:18: 21000000 INFO @ Tue, 30 Jun 2020 00:44:21: 16000000 INFO @ Tue, 30 Jun 2020 00:44:22: 11000000 INFO @ Tue, 30 Jun 2020 00:44:25: 22000000 INFO @ Tue, 30 Jun 2020 00:44:27: 17000000 INFO @ Tue, 30 Jun 2020 00:44:29: 12000000 INFO @ Tue, 30 Jun 2020 00:44:31: 23000000 INFO @ Tue, 30 Jun 2020 00:44:34: 18000000 INFO @ Tue, 30 Jun 2020 00:44:36: 13000000 INFO @ Tue, 30 Jun 2020 00:44:38: 24000000 INFO @ Tue, 30 Jun 2020 00:44:41: 19000000 INFO @ Tue, 30 Jun 2020 00:44:43: 14000000 INFO @ Tue, 30 Jun 2020 00:44:44: 25000000 INFO @ Tue, 30 Jun 2020 00:44:47: 20000000 INFO @ Tue, 30 Jun 2020 00:44:50: 15000000 INFO @ Tue, 30 Jun 2020 00:44:51: 26000000 INFO @ Tue, 30 Jun 2020 00:44:54: 21000000 INFO @ Tue, 30 Jun 2020 00:44:58: 16000000 INFO @ Tue, 30 Jun 2020 00:44:58: 27000000 INFO @ Tue, 30 Jun 2020 00:45:01: 22000000 INFO @ Tue, 30 Jun 2020 00:45:04: 28000000 INFO @ Tue, 30 Jun 2020 00:45:05: 17000000 INFO @ Tue, 30 Jun 2020 00:45:07: 23000000 INFO @ Tue, 30 Jun 2020 00:45:11: 29000000 INFO @ Tue, 30 Jun 2020 00:45:12: 18000000 INFO @ Tue, 30 Jun 2020 00:45:14: 24000000 INFO @ Tue, 30 Jun 2020 00:45:18: 30000000 INFO @ Tue, 30 Jun 2020 00:45:19: 19000000 INFO @ Tue, 30 Jun 2020 00:45:21: 25000000 INFO @ Tue, 30 Jun 2020 00:45:24: 31000000 INFO @ Tue, 30 Jun 2020 00:45:26: 20000000 INFO @ Tue, 30 Jun 2020 00:45:27: 26000000 INFO @ Tue, 30 Jun 2020 00:45:31: 32000000 INFO @ Tue, 30 Jun 2020 00:45:33: 21000000 INFO @ Tue, 30 Jun 2020 00:45:34: 27000000 INFO @ Tue, 30 Jun 2020 00:45:37: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:45:37: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:45:37: #1 total tags in treatment: 32819489 INFO @ Tue, 30 Jun 2020 00:45:37: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:45:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:45:37: #1 tags after filtering in treatment: 32819489 INFO @ Tue, 30 Jun 2020 00:45:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:45:37: #1 finished! INFO @ Tue, 30 Jun 2020 00:45:37: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:45:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:45:39: #2 number of paired peaks: 292 WARNING @ Tue, 30 Jun 2020 00:45:39: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Tue, 30 Jun 2020 00:45:39: start model_add_line... INFO @ Tue, 30 Jun 2020 00:45:40: start X-correlation... INFO @ Tue, 30 Jun 2020 00:45:40: end of X-cor INFO @ Tue, 30 Jun 2020 00:45:40: #2 finished! INFO @ Tue, 30 Jun 2020 00:45:40: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 00:45:40: #2 alternative fragment length(s) may be 3,53 bps INFO @ Tue, 30 Jun 2020 00:45:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.05_model.r WARNING @ Tue, 30 Jun 2020 00:45:40: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:45:40: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Tue, 30 Jun 2020 00:45:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:45:40: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:45:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:45:40: 22000000 INFO @ Tue, 30 Jun 2020 00:45:40: 28000000 INFO @ Tue, 30 Jun 2020 00:45:47: 23000000 INFO @ Tue, 30 Jun 2020 00:45:47: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:45:53: 30000000 INFO @ Tue, 30 Jun 2020 00:45:54: 24000000 INFO @ Tue, 30 Jun 2020 00:46:00: 31000000 INFO @ Tue, 30 Jun 2020 00:46:01: 25000000 INFO @ Tue, 30 Jun 2020 00:46:06: 32000000 INFO @ Tue, 30 Jun 2020 00:46:08: 26000000 INFO @ Tue, 30 Jun 2020 00:46:12: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:46:12: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:46:12: #1 total tags in treatment: 32819489 INFO @ Tue, 30 Jun 2020 00:46:12: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:46:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:46:13: #1 tags after filtering in treatment: 32819489 INFO @ Tue, 30 Jun 2020 00:46:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:46:13: #1 finished! INFO @ Tue, 30 Jun 2020 00:46:13: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:46:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:46:15: 27000000 INFO @ Tue, 30 Jun 2020 00:46:15: #2 number of paired peaks: 292 WARNING @ Tue, 30 Jun 2020 00:46:15: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Tue, 30 Jun 2020 00:46:15: start model_add_line... INFO @ Tue, 30 Jun 2020 00:46:15: start X-correlation... INFO @ Tue, 30 Jun 2020 00:46:15: end of X-cor INFO @ Tue, 30 Jun 2020 00:46:15: #2 finished! INFO @ Tue, 30 Jun 2020 00:46:15: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 00:46:15: #2 alternative fragment length(s) may be 3,53 bps INFO @ Tue, 30 Jun 2020 00:46:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.10_model.r WARNING @ Tue, 30 Jun 2020 00:46:15: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:46:15: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Tue, 30 Jun 2020 00:46:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:46:15: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:46:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:46:21: 28000000 INFO @ Tue, 30 Jun 2020 00:46:28: 29000000 INFO @ Tue, 30 Jun 2020 00:46:35: 30000000 INFO @ Tue, 30 Jun 2020 00:46:41: 31000000 INFO @ Tue, 30 Jun 2020 00:46:44: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:46:48: 32000000 INFO @ Tue, 30 Jun 2020 00:46:53: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:46:53: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:46:53: #1 total tags in treatment: 32819489 INFO @ Tue, 30 Jun 2020 00:46:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:46:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:46:54: #1 tags after filtering in treatment: 32819489 INFO @ Tue, 30 Jun 2020 00:46:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:46:54: #1 finished! INFO @ Tue, 30 Jun 2020 00:46:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:46:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:46:56: #2 number of paired peaks: 292 WARNING @ Tue, 30 Jun 2020 00:46:56: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Tue, 30 Jun 2020 00:46:56: start model_add_line... INFO @ Tue, 30 Jun 2020 00:46:57: start X-correlation... INFO @ Tue, 30 Jun 2020 00:46:57: end of X-cor INFO @ Tue, 30 Jun 2020 00:46:57: #2 finished! INFO @ Tue, 30 Jun 2020 00:46:57: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 00:46:57: #2 alternative fragment length(s) may be 3,53 bps INFO @ Tue, 30 Jun 2020 00:46:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.20_model.r WARNING @ Tue, 30 Jun 2020 00:46:57: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:46:57: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Tue, 30 Jun 2020 00:46:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:46:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:46:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:47:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:47:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:47:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.05_summits.bed INFO @ Tue, 30 Jun 2020 00:47:16: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11657 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:47:18: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:47:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:47:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:47:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.10_summits.bed INFO @ Tue, 30 Jun 2020 00:47:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5020 records, 4 fields): 117 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:48:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:48:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:48:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:48:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4580644/SRX4580644.20_summits.bed INFO @ Tue, 30 Jun 2020 00:48:31: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2061 records, 4 fields): 4 millis CompletedMACS2peakCalling