Job ID = 6528485 SRX = SRX751567 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T15:27:02 prefetch.2.10.7: 1) Downloading 'SRR1640727'... 2020-06-29T15:27:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T15:33:01 prefetch.2.10.7: HTTPS download succeed 2020-06-29T15:33:01 prefetch.2.10.7: 1) 'SRR1640727' was downloaded successfully Read 42375548 spots for SRR1640727/SRR1640727.sra Written 42375548 spots for SRR1640727/SRR1640727.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: 00:27:38 42375548 reads; of these: 42375548 (100.00%) were unpaired; of these: 854506 (2.02%) aligned 0 times 13175559 (31.09%) aligned exactly 1 time 28345483 (66.89%) aligned >1 times 97.98% overall alignment rate Time searching: 00:27:38 Overall time: 00:27:38 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] 10344231 / 41521042 = 0.2491 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 01:28:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.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 01:28:07: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:28:07: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:28:14: 1000000 INFO @ Tue, 30 Jun 2020 01:28:22: 2000000 INFO @ Tue, 30 Jun 2020 01:28:30: 3000000 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 01:28:36: 4000000 INFO @ Tue, 30 Jun 2020 01:28:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.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 01:28:37: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:28:37: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:28:43: 5000000 INFO @ Tue, 30 Jun 2020 01:28:44: 1000000 INFO @ Tue, 30 Jun 2020 01:28:49: 6000000 INFO @ Tue, 30 Jun 2020 01:28:50: 2000000 INFO @ Tue, 30 Jun 2020 01:28:56: 7000000 INFO @ Tue, 30 Jun 2020 01:28:56: 3000000 INFO @ Tue, 30 Jun 2020 01:29:03: 4000000 INFO @ Tue, 30 Jun 2020 01:29:03: 8000000 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 01:29:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.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 01:29:07: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:29:07: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:29:09: 5000000 INFO @ Tue, 30 Jun 2020 01:29:10: 9000000 INFO @ Tue, 30 Jun 2020 01:29:14: 1000000 INFO @ Tue, 30 Jun 2020 01:29:16: 6000000 INFO @ Tue, 30 Jun 2020 01:29:17: 10000000 INFO @ Tue, 30 Jun 2020 01:29:21: 2000000 INFO @ Tue, 30 Jun 2020 01:29:22: 7000000 INFO @ Tue, 30 Jun 2020 01:29:24: 11000000 INFO @ Tue, 30 Jun 2020 01:29:28: 3000000 INFO @ Tue, 30 Jun 2020 01:29:29: 8000000 INFO @ Tue, 30 Jun 2020 01:29:31: 12000000 INFO @ Tue, 30 Jun 2020 01:29:35: 9000000 INFO @ Tue, 30 Jun 2020 01:29:35: 4000000 INFO @ Tue, 30 Jun 2020 01:29:38: 13000000 INFO @ Tue, 30 Jun 2020 01:29:42: 10000000 INFO @ Tue, 30 Jun 2020 01:29:42: 5000000 INFO @ Tue, 30 Jun 2020 01:29:44: 14000000 INFO @ Tue, 30 Jun 2020 01:29:48: 11000000 INFO @ Tue, 30 Jun 2020 01:29:49: 6000000 INFO @ Tue, 30 Jun 2020 01:29:51: 15000000 INFO @ Tue, 30 Jun 2020 01:29:54: 12000000 INFO @ Tue, 30 Jun 2020 01:29:56: 7000000 INFO @ Tue, 30 Jun 2020 01:29:57: 16000000 INFO @ Tue, 30 Jun 2020 01:30:01: 13000000 INFO @ Tue, 30 Jun 2020 01:30:03: 8000000 INFO @ Tue, 30 Jun 2020 01:30:04: 17000000 INFO @ Tue, 30 Jun 2020 01:30:07: 14000000 INFO @ Tue, 30 Jun 2020 01:30:10: 9000000 INFO @ Tue, 30 Jun 2020 01:30:10: 18000000 INFO @ Tue, 30 Jun 2020 01:30:14: 15000000 INFO @ Tue, 30 Jun 2020 01:30:17: 19000000 INFO @ Tue, 30 Jun 2020 01:30:17: 10000000 INFO @ Tue, 30 Jun 2020 01:30:21: 16000000 INFO @ Tue, 30 Jun 2020 01:30:24: 20000000 INFO @ Tue, 30 Jun 2020 01:30:25: 11000000 INFO @ Tue, 30 Jun 2020 01:30:28: 17000000 INFO @ Tue, 30 Jun 2020 01:30:30: 21000000 INFO @ Tue, 30 Jun 2020 01:30:32: 12000000 INFO @ Tue, 30 Jun 2020 01:30:35: 18000000 INFO @ Tue, 30 Jun 2020 01:30:37: 22000000 INFO @ Tue, 30 Jun 2020 01:30:39: 13000000 INFO @ Tue, 30 Jun 2020 01:30:41: 19000000 INFO @ Tue, 30 Jun 2020 01:30:44: 23000000 INFO @ Tue, 30 Jun 2020 01:30:45: 14000000 INFO @ Tue, 30 Jun 2020 01:30:48: 20000000 INFO @ Tue, 30 Jun 2020 01:30:51: 24000000 INFO @ Tue, 30 Jun 2020 01:30:52: 15000000 INFO @ Tue, 30 Jun 2020 01:30:55: 21000000 INFO @ Tue, 30 Jun 2020 01:30:58: 25000000 INFO @ Tue, 30 Jun 2020 01:30:59: 16000000 INFO @ Tue, 30 Jun 2020 01:31:01: 22000000 INFO @ Tue, 30 Jun 2020 01:31:05: 26000000 INFO @ Tue, 30 Jun 2020 01:31:06: 17000000 INFO @ Tue, 30 Jun 2020 01:31:08: 23000000 INFO @ Tue, 30 Jun 2020 01:31:11: 27000000 INFO @ Tue, 30 Jun 2020 01:31:12: 18000000 INFO @ Tue, 30 Jun 2020 01:31:14: 24000000 INFO @ Tue, 30 Jun 2020 01:31:18: 28000000 INFO @ Tue, 30 Jun 2020 01:31:19: 19000000 INFO @ Tue, 30 Jun 2020 01:31:21: 25000000 INFO @ Tue, 30 Jun 2020 01:31:25: 29000000 INFO @ Tue, 30 Jun 2020 01:31:26: 20000000 INFO @ Tue, 30 Jun 2020 01:31:28: 26000000 INFO @ Tue, 30 Jun 2020 01:31:32: 30000000 INFO @ Tue, 30 Jun 2020 01:31:32: 21000000 INFO @ Tue, 30 Jun 2020 01:31:35: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:31:38: 31000000 INFO @ Tue, 30 Jun 2020 01:31:39: 22000000 INFO @ Tue, 30 Jun 2020 01:31:40: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:31:40: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:31:40: #1 total tags in treatment: 31176811 INFO @ Tue, 30 Jun 2020 01:31:40: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:31:40: #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 01:31:40: #1 tags after filtering in treatment: 31176811 INFO @ Tue, 30 Jun 2020 01:31:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:31:40: #1 finished! INFO @ Tue, 30 Jun 2020 01:31:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:31:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:31:41: 28000000 INFO @ Tue, 30 Jun 2020 01:31:42: #2 number of paired peaks: 121 WARNING @ Tue, 30 Jun 2020 01:31:42: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Tue, 30 Jun 2020 01:31:42: start model_add_line... INFO @ Tue, 30 Jun 2020 01:31:43: start X-correlation... INFO @ Tue, 30 Jun 2020 01:31:43: end of X-cor INFO @ Tue, 30 Jun 2020 01:31:43: #2 finished! INFO @ Tue, 30 Jun 2020 01:31:43: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 01:31:43: #2 alternative fragment length(s) may be 4,42,524 bps INFO @ Tue, 30 Jun 2020 01:31:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.05_model.r WARNING @ Tue, 30 Jun 2020 01:31:43: #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 01:31:43: #2 You may need to consider one of the other alternative d(s): 4,42,524 WARNING @ Tue, 30 Jun 2020 01:31:43: #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 01:31:43: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:31:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:31:45: 23000000 INFO @ Tue, 30 Jun 2020 01:31:48: 29000000 INFO @ Tue, 30 Jun 2020 01:31:51: 24000000 INFO @ Tue, 30 Jun 2020 01:31:54: 30000000 INFO @ Tue, 30 Jun 2020 01:31:57: 25000000 INFO @ Tue, 30 Jun 2020 01:32:01: 31000000 INFO @ Tue, 30 Jun 2020 01:32:02: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:32:02: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:32:02: #1 total tags in treatment: 31176811 INFO @ Tue, 30 Jun 2020 01:32:02: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:32:02: #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 01:32:03: #1 tags after filtering in treatment: 31176811 INFO @ Tue, 30 Jun 2020 01:32:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:32:03: #1 finished! INFO @ Tue, 30 Jun 2020 01:32:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:32:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:32:03: 26000000 INFO @ Tue, 30 Jun 2020 01:32:05: #2 number of paired peaks: 121 WARNING @ Tue, 30 Jun 2020 01:32:05: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Tue, 30 Jun 2020 01:32:05: start model_add_line... INFO @ Tue, 30 Jun 2020 01:32:05: start X-correlation... INFO @ Tue, 30 Jun 2020 01:32:05: end of X-cor INFO @ Tue, 30 Jun 2020 01:32:05: #2 finished! INFO @ Tue, 30 Jun 2020 01:32:05: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 01:32:05: #2 alternative fragment length(s) may be 4,42,524 bps INFO @ Tue, 30 Jun 2020 01:32:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.10_model.r WARNING @ Tue, 30 Jun 2020 01:32:05: #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 01:32:05: #2 You may need to consider one of the other alternative d(s): 4,42,524 WARNING @ Tue, 30 Jun 2020 01:32:05: #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 01:32:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:32:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:32:09: 27000000 INFO @ Tue, 30 Jun 2020 01:32:15: 28000000 INFO @ Tue, 30 Jun 2020 01:32:21: 29000000 INFO @ Tue, 30 Jun 2020 01:32:28: 30000000 INFO @ Tue, 30 Jun 2020 01:32:34: 31000000 INFO @ Tue, 30 Jun 2020 01:32:34: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:32:35: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:32:35: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:32:35: #1 total tags in treatment: 31176811 INFO @ Tue, 30 Jun 2020 01:32:35: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:32:35: #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 01:32:36: #1 tags after filtering in treatment: 31176811 INFO @ Tue, 30 Jun 2020 01:32:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:32:36: #1 finished! INFO @ Tue, 30 Jun 2020 01:32:36: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:32:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:32:38: #2 number of paired peaks: 121 WARNING @ Tue, 30 Jun 2020 01:32:38: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Tue, 30 Jun 2020 01:32:38: start model_add_line... INFO @ Tue, 30 Jun 2020 01:32:38: start X-correlation... INFO @ Tue, 30 Jun 2020 01:32:38: end of X-cor INFO @ Tue, 30 Jun 2020 01:32:38: #2 finished! INFO @ Tue, 30 Jun 2020 01:32:38: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 01:32:38: #2 alternative fragment length(s) may be 4,42,524 bps INFO @ Tue, 30 Jun 2020 01:32:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.20_model.r WARNING @ Tue, 30 Jun 2020 01:32:38: #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 01:32:38: #2 You may need to consider one of the other alternative d(s): 4,42,524 WARNING @ Tue, 30 Jun 2020 01:32:38: #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 01:32:38: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:32:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:32:56: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:33:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:33:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:33:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.05_summits.bed INFO @ Tue, 30 Jun 2020 01:33:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (12232 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:33:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:33:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:33:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.10_summits.bed INFO @ Tue, 30 Jun 2020 01:33:26: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2997 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:33:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:33:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:33:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:33:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX751567/SRX751567.20_summits.bed INFO @ Tue, 30 Jun 2020 01:33:57: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1069 records, 4 fields): 3 millis CompletedMACS2peakCalling