Job ID = 6528486 SRX = SRX751569 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T15:26:32 prefetch.2.10.7: 1) Downloading 'SRR1640729'... 2020-06-29T15:26:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T15:31:42 prefetch.2.10.7: HTTPS download succeed 2020-06-29T15:31:42 prefetch.2.10.7: 1) 'SRR1640729' was downloaded successfully Read 41787348 spots for SRR1640729/SRR1640729.sra Written 41787348 spots for SRR1640729/SRR1640729.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: 00:28:23 41787348 reads; of these: 41787348 (100.00%) were unpaired; of these: 796709 (1.91%) aligned 0 times 12647852 (30.27%) aligned exactly 1 time 28342787 (67.83%) aligned >1 times 98.09% overall alignment rate Time searching: 00:28:23 Overall time: 00:28:23 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] 11078417 / 40990639 = 0.2703 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 01:26:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.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 01:26:50: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:26:50: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:26:56: 1000000 INFO @ Tue, 30 Jun 2020 01:27:01: 2000000 INFO @ Tue, 30 Jun 2020 01:27:07: 3000000 INFO @ Tue, 30 Jun 2020 01:27:13: 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 01:27:18: 5000000 INFO @ Tue, 30 Jun 2020 01:27:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.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 01:27:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:27:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:27:25: 6000000 INFO @ Tue, 30 Jun 2020 01:27:27: 1000000 INFO @ Tue, 30 Jun 2020 01:27:31: 7000000 INFO @ Tue, 30 Jun 2020 01:27:33: 2000000 INFO @ Tue, 30 Jun 2020 01:27:38: 8000000 INFO @ Tue, 30 Jun 2020 01:27:39: 3000000 INFO @ Tue, 30 Jun 2020 01:27:44: 9000000 INFO @ Tue, 30 Jun 2020 01:27:46: 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 01:27:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.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 01:27:50: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:27:50: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:27:51: 10000000 INFO @ Tue, 30 Jun 2020 01:27:52: 5000000 INFO @ Tue, 30 Jun 2020 01:27:57: 1000000 INFO @ Tue, 30 Jun 2020 01:27:58: 6000000 INFO @ Tue, 30 Jun 2020 01:27:58: 11000000 INFO @ Tue, 30 Jun 2020 01:28:04: 2000000 INFO @ Tue, 30 Jun 2020 01:28:05: 7000000 INFO @ Tue, 30 Jun 2020 01:28:06: 12000000 INFO @ Tue, 30 Jun 2020 01:28:11: 3000000 INFO @ Tue, 30 Jun 2020 01:28:11: 8000000 INFO @ Tue, 30 Jun 2020 01:28:13: 13000000 INFO @ Tue, 30 Jun 2020 01:28:18: 9000000 INFO @ Tue, 30 Jun 2020 01:28:18: 4000000 INFO @ Tue, 30 Jun 2020 01:28:20: 14000000 INFO @ Tue, 30 Jun 2020 01:28:24: 10000000 INFO @ Tue, 30 Jun 2020 01:28:25: 5000000 INFO @ Tue, 30 Jun 2020 01:28:27: 15000000 INFO @ Tue, 30 Jun 2020 01:28:31: 11000000 INFO @ Tue, 30 Jun 2020 01:28:32: 6000000 INFO @ Tue, 30 Jun 2020 01:28:34: 16000000 INFO @ Tue, 30 Jun 2020 01:28:37: 12000000 INFO @ Tue, 30 Jun 2020 01:28:39: 7000000 INFO @ Tue, 30 Jun 2020 01:28:41: 17000000 INFO @ Tue, 30 Jun 2020 01:28:44: 13000000 INFO @ Tue, 30 Jun 2020 01:28:47: 8000000 INFO @ Tue, 30 Jun 2020 01:28:48: 18000000 INFO @ Tue, 30 Jun 2020 01:28:50: 14000000 INFO @ Tue, 30 Jun 2020 01:28:54: 9000000 INFO @ Tue, 30 Jun 2020 01:28:55: 19000000 INFO @ Tue, 30 Jun 2020 01:28:56: 15000000 INFO @ Tue, 30 Jun 2020 01:29:01: 10000000 INFO @ Tue, 30 Jun 2020 01:29:02: 20000000 INFO @ Tue, 30 Jun 2020 01:29:03: 16000000 INFO @ Tue, 30 Jun 2020 01:29:08: 11000000 INFO @ Tue, 30 Jun 2020 01:29:09: 21000000 INFO @ Tue, 30 Jun 2020 01:29:09: 17000000 INFO @ Tue, 30 Jun 2020 01:29:15: 12000000 INFO @ Tue, 30 Jun 2020 01:29:16: 18000000 INFO @ Tue, 30 Jun 2020 01:29:16: 22000000 INFO @ Tue, 30 Jun 2020 01:29:22: 19000000 INFO @ Tue, 30 Jun 2020 01:29:22: 13000000 INFO @ Tue, 30 Jun 2020 01:29:23: 23000000 INFO @ Tue, 30 Jun 2020 01:29:29: 20000000 INFO @ Tue, 30 Jun 2020 01:29:29: 14000000 INFO @ Tue, 30 Jun 2020 01:29:30: 24000000 INFO @ Tue, 30 Jun 2020 01:29:35: 21000000 INFO @ Tue, 30 Jun 2020 01:29:36: 15000000 INFO @ Tue, 30 Jun 2020 01:29:37: 25000000 INFO @ Tue, 30 Jun 2020 01:29:42: 22000000 INFO @ Tue, 30 Jun 2020 01:29:43: 16000000 INFO @ Tue, 30 Jun 2020 01:29:44: 26000000 INFO @ Tue, 30 Jun 2020 01:29:48: 23000000 INFO @ Tue, 30 Jun 2020 01:29:50: 17000000 INFO @ Tue, 30 Jun 2020 01:29:51: 27000000 INFO @ Tue, 30 Jun 2020 01:29:54: 24000000 INFO @ Tue, 30 Jun 2020 01:29:57: 18000000 INFO @ Tue, 30 Jun 2020 01:29:58: 28000000 INFO @ Tue, 30 Jun 2020 01:30:01: 25000000 INFO @ Tue, 30 Jun 2020 01:30:04: 19000000 INFO @ Tue, 30 Jun 2020 01:30:04: 29000000 INFO @ Tue, 30 Jun 2020 01:30:07: 26000000 INFO @ Tue, 30 Jun 2020 01:30:11: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:30:11: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:30:11: #1 total tags in treatment: 29912222 INFO @ Tue, 30 Jun 2020 01:30:11: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:30:11: #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 01:30:11: 20000000 INFO @ Tue, 30 Jun 2020 01:30:11: #1 tags after filtering in treatment: 29912222 INFO @ Tue, 30 Jun 2020 01:30:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:30:11: #1 finished! INFO @ Tue, 30 Jun 2020 01:30:11: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:30:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:30:13: 27000000 INFO @ Tue, 30 Jun 2020 01:30:13: #2 number of paired peaks: 252 WARNING @ Tue, 30 Jun 2020 01:30:13: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Tue, 30 Jun 2020 01:30:13: start model_add_line... INFO @ Tue, 30 Jun 2020 01:30:14: start X-correlation... INFO @ Tue, 30 Jun 2020 01:30:14: end of X-cor INFO @ Tue, 30 Jun 2020 01:30:14: #2 finished! INFO @ Tue, 30 Jun 2020 01:30:14: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 01:30:14: #2 alternative fragment length(s) may be 3,28,42,515 bps INFO @ Tue, 30 Jun 2020 01:30:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.05_model.r WARNING @ Tue, 30 Jun 2020 01:30:14: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:30:14: #2 You may need to consider one of the other alternative d(s): 3,28,42,515 WARNING @ Tue, 30 Jun 2020 01:30:14: #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 01:30:14: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:30:14: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:30:18: 21000000 INFO @ Tue, 30 Jun 2020 01:30:19: 28000000 INFO @ Tue, 30 Jun 2020 01:30:25: 22000000 INFO @ Tue, 30 Jun 2020 01:30:25: 29000000 INFO @ Tue, 30 Jun 2020 01:30:31: 23000000 INFO @ Tue, 30 Jun 2020 01:30:31: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:30:31: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:30:31: #1 total tags in treatment: 29912222 INFO @ Tue, 30 Jun 2020 01:30:31: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:30:31: #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 01:30:32: #1 tags after filtering in treatment: 29912222 INFO @ Tue, 30 Jun 2020 01:30:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:30:32: #1 finished! INFO @ Tue, 30 Jun 2020 01:30:32: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:30:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:30:34: #2 number of paired peaks: 252 WARNING @ Tue, 30 Jun 2020 01:30:34: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Tue, 30 Jun 2020 01:30:34: start model_add_line... INFO @ Tue, 30 Jun 2020 01:30:34: start X-correlation... INFO @ Tue, 30 Jun 2020 01:30:34: end of X-cor INFO @ Tue, 30 Jun 2020 01:30:34: #2 finished! INFO @ Tue, 30 Jun 2020 01:30:34: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 01:30:34: #2 alternative fragment length(s) may be 3,28,42,515 bps INFO @ Tue, 30 Jun 2020 01:30:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.10_model.r WARNING @ Tue, 30 Jun 2020 01:30:34: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:30:34: #2 You may need to consider one of the other alternative d(s): 3,28,42,515 WARNING @ Tue, 30 Jun 2020 01:30:34: #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 01:30:34: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:30:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:30:37: 24000000 INFO @ Tue, 30 Jun 2020 01:30:43: 25000000 INFO @ Tue, 30 Jun 2020 01:30:49: 26000000 INFO @ Tue, 30 Jun 2020 01:30:55: 27000000 INFO @ Tue, 30 Jun 2020 01:31:00: 28000000 INFO @ Tue, 30 Jun 2020 01:31:04: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:31:06: 29000000 INFO @ Tue, 30 Jun 2020 01:31:11: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:31:11: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:31:11: #1 total tags in treatment: 29912222 INFO @ Tue, 30 Jun 2020 01:31:11: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:31:11: #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 01:31:11: #1 tags after filtering in treatment: 29912222 INFO @ Tue, 30 Jun 2020 01:31:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:31:11: #1 finished! INFO @ Tue, 30 Jun 2020 01:31:11: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:31:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:31:13: #2 number of paired peaks: 252 WARNING @ Tue, 30 Jun 2020 01:31:13: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Tue, 30 Jun 2020 01:31:13: start model_add_line... INFO @ Tue, 30 Jun 2020 01:31:14: start X-correlation... INFO @ Tue, 30 Jun 2020 01:31:14: end of X-cor INFO @ Tue, 30 Jun 2020 01:31:14: #2 finished! INFO @ Tue, 30 Jun 2020 01:31:14: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 01:31:14: #2 alternative fragment length(s) may be 3,28,42,515 bps INFO @ Tue, 30 Jun 2020 01:31:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.20_model.r WARNING @ Tue, 30 Jun 2020 01:31:14: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:31:14: #2 You may need to consider one of the other alternative d(s): 3,28,42,515 WARNING @ Tue, 30 Jun 2020 01:31:14: #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 01:31:14: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:31:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:31:24: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:31:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:31:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:31:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.05_summits.bed INFO @ Tue, 30 Jun 2020 01:31:30: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11082 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:31:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:31:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:31:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.10_summits.bed INFO @ Tue, 30 Jun 2020 01:31:51: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2984 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:32:03: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:32:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:32:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:32:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX751569/SRX751569.20_summits.bed INFO @ Tue, 30 Jun 2020 01:32:29: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1159 records, 4 fields): 3 millis CompletedMACS2peakCalling