Job ID = 6527876 SRX = SRX287991 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:17:36 prefetch.2.10.7: 1) Downloading 'SRR870180'... 2020-06-29T14:17:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:19:55 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:19:55 prefetch.2.10.7: 1) 'SRR870180' was downloaded successfully Read 26924228 spots for SRR870180/SRR870180.sra Written 26924228 spots for SRR870180/SRR870180.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: 00:12:13 26924228 reads; of these: 26924228 (100.00%) were unpaired; of these: 1125804 (4.18%) aligned 0 times 17097062 (63.50%) aligned exactly 1 time 8701362 (32.32%) aligned >1 times 95.82% overall alignment rate Time searching: 00:12:13 Overall time: 00:12:13 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 12 files... [bam_rmdupse_core] 3992318 / 25798424 = 0.1548 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 23:49:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.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 23:49:27: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:49:27: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:49:36: 1000000 INFO @ Mon, 29 Jun 2020 23:49:46: 2000000 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 23:49:56: 3000000 INFO @ Mon, 29 Jun 2020 23:49:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.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 23:49:57: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:49:57: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:50:06: 4000000 INFO @ Mon, 29 Jun 2020 23:50:07: 1000000 INFO @ Mon, 29 Jun 2020 23:50:16: 5000000 INFO @ Mon, 29 Jun 2020 23:50:17: 2000000 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 23:50:26: 6000000 INFO @ Mon, 29 Jun 2020 23:50:27: 3000000 INFO @ Mon, 29 Jun 2020 23:50:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.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 23:50:27: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:50:27: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:50:36: 7000000 INFO @ Mon, 29 Jun 2020 23:50:37: 4000000 INFO @ Mon, 29 Jun 2020 23:50:37: 1000000 INFO @ Mon, 29 Jun 2020 23:50:46: 8000000 INFO @ Mon, 29 Jun 2020 23:50:47: 5000000 INFO @ Mon, 29 Jun 2020 23:50:47: 2000000 INFO @ Mon, 29 Jun 2020 23:50:56: 9000000 INFO @ Mon, 29 Jun 2020 23:50:57: 6000000 INFO @ Mon, 29 Jun 2020 23:50:58: 3000000 INFO @ Mon, 29 Jun 2020 23:51:07: 10000000 INFO @ Mon, 29 Jun 2020 23:51:08: 7000000 INFO @ Mon, 29 Jun 2020 23:51:08: 4000000 INFO @ Mon, 29 Jun 2020 23:51:17: 11000000 INFO @ Mon, 29 Jun 2020 23:51:18: 8000000 INFO @ Mon, 29 Jun 2020 23:51:18: 5000000 INFO @ Mon, 29 Jun 2020 23:51:27: 12000000 INFO @ Mon, 29 Jun 2020 23:51:29: 6000000 INFO @ Mon, 29 Jun 2020 23:51:29: 9000000 INFO @ Mon, 29 Jun 2020 23:51:38: 13000000 INFO @ Mon, 29 Jun 2020 23:51:39: 10000000 INFO @ Mon, 29 Jun 2020 23:51:39: 7000000 INFO @ Mon, 29 Jun 2020 23:51:48: 14000000 INFO @ Mon, 29 Jun 2020 23:51:49: 8000000 INFO @ Mon, 29 Jun 2020 23:51:49: 11000000 INFO @ Mon, 29 Jun 2020 23:51:58: 15000000 INFO @ Mon, 29 Jun 2020 23:52:00: 12000000 INFO @ Mon, 29 Jun 2020 23:52:00: 9000000 INFO @ Mon, 29 Jun 2020 23:52:09: 16000000 INFO @ Mon, 29 Jun 2020 23:52:10: 13000000 INFO @ Mon, 29 Jun 2020 23:52:10: 10000000 INFO @ Mon, 29 Jun 2020 23:52:19: 17000000 INFO @ Mon, 29 Jun 2020 23:52:20: 14000000 INFO @ Mon, 29 Jun 2020 23:52:20: 11000000 INFO @ Mon, 29 Jun 2020 23:52:29: 18000000 INFO @ Mon, 29 Jun 2020 23:52:30: 15000000 INFO @ Mon, 29 Jun 2020 23:52:30: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:52:40: 19000000 INFO @ Mon, 29 Jun 2020 23:52:40: 13000000 INFO @ Mon, 29 Jun 2020 23:52:40: 16000000 INFO @ Mon, 29 Jun 2020 23:52:50: 20000000 INFO @ Mon, 29 Jun 2020 23:52:50: 14000000 INFO @ Mon, 29 Jun 2020 23:52:51: 17000000 INFO @ Mon, 29 Jun 2020 23:53:00: 21000000 INFO @ Mon, 29 Jun 2020 23:53:00: 15000000 INFO @ Mon, 29 Jun 2020 23:53:01: 18000000 INFO @ Mon, 29 Jun 2020 23:53:08: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:53:08: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:53:08: #1 total tags in treatment: 21806106 INFO @ Mon, 29 Jun 2020 23:53:08: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:53:08: #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 23:53:08: #1 tags after filtering in treatment: 21806106 INFO @ Mon, 29 Jun 2020 23:53:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:53:08: #1 finished! INFO @ Mon, 29 Jun 2020 23:53:08: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:53:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:53:10: #2 number of paired peaks: 167 WARNING @ Mon, 29 Jun 2020 23:53:10: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Mon, 29 Jun 2020 23:53:10: start model_add_line... INFO @ Mon, 29 Jun 2020 23:53:10: start X-correlation... INFO @ Mon, 29 Jun 2020 23:53:10: end of X-cor INFO @ Mon, 29 Jun 2020 23:53:10: #2 finished! INFO @ Mon, 29 Jun 2020 23:53:10: #2 predicted fragment length is 41 bps INFO @ Mon, 29 Jun 2020 23:53:10: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 29 Jun 2020 23:53:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.05_model.r WARNING @ Mon, 29 Jun 2020 23:53:10: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:53:10: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 29 Jun 2020 23:53:10: #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 23:53:10: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:53:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:53:10: 16000000 INFO @ Mon, 29 Jun 2020 23:53:11: 19000000 INFO @ Mon, 29 Jun 2020 23:53:20: 17000000 INFO @ Mon, 29 Jun 2020 23:53:20: 20000000 INFO @ Mon, 29 Jun 2020 23:53:30: 18000000 INFO @ Mon, 29 Jun 2020 23:53:30: 21000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:53:38: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:53:38: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:53:38: #1 total tags in treatment: 21806106 INFO @ Mon, 29 Jun 2020 23:53:38: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:53:38: #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 23:53:38: #1 tags after filtering in treatment: 21806106 INFO @ Mon, 29 Jun 2020 23:53:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:53:38: #1 finished! INFO @ Mon, 29 Jun 2020 23:53:38: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:53:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:53:39: 19000000 INFO @ Mon, 29 Jun 2020 23:53:40: #2 number of paired peaks: 167 WARNING @ Mon, 29 Jun 2020 23:53:40: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Mon, 29 Jun 2020 23:53:40: start model_add_line... INFO @ Mon, 29 Jun 2020 23:53:40: start X-correlation... INFO @ Mon, 29 Jun 2020 23:53:40: end of X-cor INFO @ Mon, 29 Jun 2020 23:53:40: #2 finished! INFO @ Mon, 29 Jun 2020 23:53:40: #2 predicted fragment length is 41 bps INFO @ Mon, 29 Jun 2020 23:53:40: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 29 Jun 2020 23:53:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.10_model.r WARNING @ Mon, 29 Jun 2020 23:53:40: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:53:40: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 29 Jun 2020 23:53:40: #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 23:53:40: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:53:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:53:46: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:53:49: 20000000 INFO @ Mon, 29 Jun 2020 23:53:58: 21000000 INFO @ Mon, 29 Jun 2020 23:54:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:54:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:54:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.05_summits.bed INFO @ Mon, 29 Jun 2020 23:54:05: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2224 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:54:06: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:54:06: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:54:06: #1 total tags in treatment: 21806106 INFO @ Mon, 29 Jun 2020 23:54:06: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:54:06: #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 23:54:06: #1 tags after filtering in treatment: 21806106 INFO @ Mon, 29 Jun 2020 23:54:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:54:06: #1 finished! INFO @ Mon, 29 Jun 2020 23:54:06: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:54:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:54:08: #2 number of paired peaks: 167 WARNING @ Mon, 29 Jun 2020 23:54:08: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Mon, 29 Jun 2020 23:54:08: start model_add_line... INFO @ Mon, 29 Jun 2020 23:54:08: start X-correlation... INFO @ Mon, 29 Jun 2020 23:54:08: end of X-cor INFO @ Mon, 29 Jun 2020 23:54:08: #2 finished! INFO @ Mon, 29 Jun 2020 23:54:08: #2 predicted fragment length is 41 bps INFO @ Mon, 29 Jun 2020 23:54:08: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 29 Jun 2020 23:54:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.20_model.r WARNING @ Mon, 29 Jun 2020 23:54:08: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:54:08: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 29 Jun 2020 23:54:08: #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 23:54:08: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:54:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:54:15: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:54:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:54:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:54:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.10_summits.bed INFO @ Mon, 29 Jun 2020 23:54:34: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1883 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:54:43: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:55:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:55:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:55:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287991/SRX287991.20_summits.bed INFO @ Mon, 29 Jun 2020 23:55:02: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1456 records, 4 fields): 4 millis CompletedMACS2peakCalling