Job ID = 6528408 SRX = SRX5827845 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:53:29 prefetch.2.10.7: 1) Downloading 'SRR9051596'... 2020-06-29T14:53:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T15:00:25 prefetch.2.10.7: HTTPS download succeed 2020-06-29T15:00:25 prefetch.2.10.7: 1) 'SRR9051596' was downloaded successfully 2020-06-29T15:00:25 prefetch.2.10.7: 'SRR9051596' has 0 unresolved dependencies Read 75603991 spots for SRR9051596/SRR9051596.sra Written 75603991 spots for SRR9051596/SRR9051596.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: 00:20:48 75603991 reads; of these: 75603991 (100.00%) were unpaired; of these: 11647903 (15.41%) aligned 0 times 48250884 (63.82%) aligned exactly 1 time 15705204 (20.77%) aligned >1 times 84.59% overall alignment rate Time searching: 00:20:48 Overall time: 00:20:49 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 28 files... [bam_rmdupse_core] 39789678 / 63956088 = 0.6221 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 01:02:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.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 01:02:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:02:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:02:49: 1000000 INFO @ Tue, 30 Jun 2020 01:02:54: 2000000 INFO @ Tue, 30 Jun 2020 01:03:00: 3000000 INFO @ Tue, 30 Jun 2020 01:03:05: 4000000 INFO @ Tue, 30 Jun 2020 01:03:10: 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 @ Tue, 30 Jun 2020 01:03:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.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 01:03:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:03:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:03:16: 6000000 INFO @ Tue, 30 Jun 2020 01:03:19: 1000000 INFO @ Tue, 30 Jun 2020 01:03:21: 7000000 INFO @ Tue, 30 Jun 2020 01:03:24: 2000000 INFO @ Tue, 30 Jun 2020 01:03:27: 8000000 INFO @ Tue, 30 Jun 2020 01:03:30: 3000000 INFO @ Tue, 30 Jun 2020 01:03:33: 9000000 INFO @ Tue, 30 Jun 2020 01:03:35: 4000000 INFO @ Tue, 30 Jun 2020 01:03:38: 10000000 INFO @ Tue, 30 Jun 2020 01:03:41: 5000000 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 01:03:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.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 01:03:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:03:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:03:44: 11000000 INFO @ Tue, 30 Jun 2020 01:03:46: 6000000 INFO @ Tue, 30 Jun 2020 01:03:49: 1000000 INFO @ Tue, 30 Jun 2020 01:03:49: 12000000 INFO @ Tue, 30 Jun 2020 01:03:52: 7000000 INFO @ Tue, 30 Jun 2020 01:03:55: 13000000 INFO @ Tue, 30 Jun 2020 01:03:55: 2000000 INFO @ Tue, 30 Jun 2020 01:03:58: 8000000 INFO @ Tue, 30 Jun 2020 01:04:00: 14000000 INFO @ Tue, 30 Jun 2020 01:04:01: 3000000 INFO @ Tue, 30 Jun 2020 01:04:03: 9000000 INFO @ Tue, 30 Jun 2020 01:04:06: 15000000 INFO @ Tue, 30 Jun 2020 01:04:07: 4000000 INFO @ Tue, 30 Jun 2020 01:04:09: 10000000 INFO @ Tue, 30 Jun 2020 01:04:12: 16000000 INFO @ Tue, 30 Jun 2020 01:04:13: 5000000 INFO @ Tue, 30 Jun 2020 01:04:15: 11000000 INFO @ Tue, 30 Jun 2020 01:04:17: 17000000 INFO @ Tue, 30 Jun 2020 01:04:19: 6000000 INFO @ Tue, 30 Jun 2020 01:04:20: 12000000 INFO @ Tue, 30 Jun 2020 01:04:23: 18000000 INFO @ Tue, 30 Jun 2020 01:04:24: 7000000 INFO @ Tue, 30 Jun 2020 01:04:26: 13000000 INFO @ Tue, 30 Jun 2020 01:04:28: 19000000 INFO @ Tue, 30 Jun 2020 01:04:30: 8000000 INFO @ Tue, 30 Jun 2020 01:04:32: 14000000 INFO @ Tue, 30 Jun 2020 01:04:34: 20000000 INFO @ Tue, 30 Jun 2020 01:04:36: 9000000 INFO @ Tue, 30 Jun 2020 01:04:37: 15000000 INFO @ Tue, 30 Jun 2020 01:04:40: 21000000 INFO @ Tue, 30 Jun 2020 01:04:42: 10000000 INFO @ Tue, 30 Jun 2020 01:04:43: 16000000 INFO @ Tue, 30 Jun 2020 01:04:45: 22000000 INFO @ Tue, 30 Jun 2020 01:04:47: 11000000 INFO @ Tue, 30 Jun 2020 01:04:49: 17000000 INFO @ Tue, 30 Jun 2020 01:04:51: 23000000 INFO @ Tue, 30 Jun 2020 01:04:53: 12000000 INFO @ Tue, 30 Jun 2020 01:04:54: 18000000 INFO @ Tue, 30 Jun 2020 01:04:56: 24000000 INFO @ Tue, 30 Jun 2020 01:04:57: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 01:04:57: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 01:04:57: #1 total tags in treatment: 24166410 INFO @ Tue, 30 Jun 2020 01:04:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:04:57: #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 01:04:58: #1 tags after filtering in treatment: 24166410 INFO @ Tue, 30 Jun 2020 01:04:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:04:58: #1 finished! INFO @ Tue, 30 Jun 2020 01:04:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:04:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:04:58: 13000000 INFO @ Tue, 30 Jun 2020 01:04:59: #2 number of paired peaks: 128 WARNING @ Tue, 30 Jun 2020 01:04:59: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Tue, 30 Jun 2020 01:04:59: start model_add_line... INFO @ Tue, 30 Jun 2020 01:05:00: start X-correlation... INFO @ Tue, 30 Jun 2020 01:05:00: 19000000 INFO @ Tue, 30 Jun 2020 01:05:00: end of X-cor INFO @ Tue, 30 Jun 2020 01:05:00: #2 finished! INFO @ Tue, 30 Jun 2020 01:05:00: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 01:05:00: #2 alternative fragment length(s) may be 4,44 bps INFO @ Tue, 30 Jun 2020 01:05:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.05_model.r WARNING @ Tue, 30 Jun 2020 01:05:00: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:05:00: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Tue, 30 Jun 2020 01:05:00: #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 01:05:00: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:05:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:05:04: 14000000 INFO @ Tue, 30 Jun 2020 01:05:05: 20000000 INFO @ Tue, 30 Jun 2020 01:05:09: 15000000 INFO @ Tue, 30 Jun 2020 01:05:11: 21000000 INFO @ Tue, 30 Jun 2020 01:05:15: 16000000 INFO @ Tue, 30 Jun 2020 01:05:16: 22000000 INFO @ Tue, 30 Jun 2020 01:05:20: 17000000 INFO @ Tue, 30 Jun 2020 01:05:22: 23000000 INFO @ Tue, 30 Jun 2020 01:05:26: 18000000 INFO @ Tue, 30 Jun 2020 01:05:27: 24000000 INFO @ Tue, 30 Jun 2020 01:05:28: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 01:05:28: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 01:05:28: #1 total tags in treatment: 24166410 INFO @ Tue, 30 Jun 2020 01:05:28: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:05:28: #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 01:05:29: #1 tags after filtering in treatment: 24166410 INFO @ Tue, 30 Jun 2020 01:05:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:05:29: #1 finished! INFO @ Tue, 30 Jun 2020 01:05:29: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:05:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:05:30: #2 number of paired peaks: 128 WARNING @ Tue, 30 Jun 2020 01:05:30: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Tue, 30 Jun 2020 01:05:30: start model_add_line... INFO @ Tue, 30 Jun 2020 01:05:31: start X-correlation... INFO @ Tue, 30 Jun 2020 01:05:31: end of X-cor INFO @ Tue, 30 Jun 2020 01:05:31: #2 finished! INFO @ Tue, 30 Jun 2020 01:05:31: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 01:05:31: #2 alternative fragment length(s) may be 4,44 bps INFO @ Tue, 30 Jun 2020 01:05:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.10_model.r WARNING @ Tue, 30 Jun 2020 01:05:31: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:05:31: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Tue, 30 Jun 2020 01:05:31: #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 01:05:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:05:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:05:31: 19000000 INFO @ Tue, 30 Jun 2020 01:05:36: 20000000 INFO @ Tue, 30 Jun 2020 01:05:42: 21000000 INFO @ Tue, 30 Jun 2020 01:05:45: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:05:48: 22000000 INFO @ Tue, 30 Jun 2020 01:05:53: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:05:59: 24000000 INFO @ Tue, 30 Jun 2020 01:06:00: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 01:06:00: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 01:06:00: #1 total tags in treatment: 24166410 INFO @ Tue, 30 Jun 2020 01:06:00: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:06:00: #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 01:06:00: #1 tags after filtering in treatment: 24166410 INFO @ Tue, 30 Jun 2020 01:06:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:06:00: #1 finished! INFO @ Tue, 30 Jun 2020 01:06:00: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:06:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:06:02: #2 number of paired peaks: 128 WARNING @ Tue, 30 Jun 2020 01:06:02: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Tue, 30 Jun 2020 01:06:02: start model_add_line... INFO @ Tue, 30 Jun 2020 01:06:02: start X-correlation... INFO @ Tue, 30 Jun 2020 01:06:02: end of X-cor INFO @ Tue, 30 Jun 2020 01:06:02: #2 finished! INFO @ Tue, 30 Jun 2020 01:06:02: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 01:06:02: #2 alternative fragment length(s) may be 4,44 bps INFO @ Tue, 30 Jun 2020 01:06:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.20_model.r WARNING @ Tue, 30 Jun 2020 01:06:02: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:06:02: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Tue, 30 Jun 2020 01:06:02: #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 01:06:02: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:06:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:06:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:06:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:06:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.05_summits.bed INFO @ Tue, 30 Jun 2020 01:06:08: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2315 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:06:18: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:06:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:06:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:06:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.10_summits.bed INFO @ Tue, 30 Jun 2020 01:06:41: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1736 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:06:46: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:07:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:07:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:07:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827845/SRX5827845.20_summits.bed INFO @ Tue, 30 Jun 2020 01:07:10: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1077 records, 4 fields): 2 millis CompletedMACS2peakCalling