Job ID = 6454632 SRX = SRX2422636 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:28:44 prefetch.2.10.7: 1) Downloading 'SRR5110250'... 2020-06-21T09:28:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:33:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:33:12 prefetch.2.10.7: 1) 'SRR5110250' was downloaded successfully Read 21681801 spots for SRR5110250/SRR5110250.sra Written 21681801 spots for SRR5110250/SRR5110250.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: 00:07:40 21681801 reads; of these: 21681801 (100.00%) were unpaired; of these: 586232 (2.70%) aligned 0 times 14500584 (66.88%) aligned exactly 1 time 6594985 (30.42%) aligned >1 times 97.30% overall alignment rate Time searching: 00:07:40 Overall time: 00:07:40 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3002270 / 21095569 = 0.1423 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 @ Sun, 21 Jun 2020 18:48:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.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 @ Sun, 21 Jun 2020 18:48:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:20: 1000000 INFO @ Sun, 21 Jun 2020 18:48:26: 2000000 INFO @ Sun, 21 Jun 2020 18:48:33: 3000000 INFO @ Sun, 21 Jun 2020 18:48:40: 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 @ Sun, 21 Jun 2020 18:48:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.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 @ Sun, 21 Jun 2020 18:48:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:47: 5000000 INFO @ Sun, 21 Jun 2020 18:48:51: 1000000 INFO @ Sun, 21 Jun 2020 18:48:55: 6000000 INFO @ Sun, 21 Jun 2020 18:48:58: 2000000 INFO @ Sun, 21 Jun 2020 18:49:02: 7000000 INFO @ Sun, 21 Jun 2020 18:49:06: 3000000 INFO @ Sun, 21 Jun 2020 18:49:10: 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 @ Sun, 21 Jun 2020 18:49:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.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 @ Sun, 21 Jun 2020 18:49:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:13: 4000000 INFO @ Sun, 21 Jun 2020 18:49:18: 9000000 INFO @ Sun, 21 Jun 2020 18:49:21: 1000000 INFO @ Sun, 21 Jun 2020 18:49:21: 5000000 INFO @ Sun, 21 Jun 2020 18:49:26: 10000000 INFO @ Sun, 21 Jun 2020 18:49:29: 2000000 INFO @ Sun, 21 Jun 2020 18:49:29: 6000000 INFO @ Sun, 21 Jun 2020 18:49:34: 11000000 INFO @ Sun, 21 Jun 2020 18:49:37: 7000000 INFO @ Sun, 21 Jun 2020 18:49:37: 3000000 INFO @ Sun, 21 Jun 2020 18:49:41: 12000000 INFO @ Sun, 21 Jun 2020 18:49:44: 4000000 INFO @ Sun, 21 Jun 2020 18:49:44: 8000000 INFO @ Sun, 21 Jun 2020 18:49:49: 13000000 INFO @ Sun, 21 Jun 2020 18:49:52: 9000000 INFO @ Sun, 21 Jun 2020 18:49:52: 5000000 INFO @ Sun, 21 Jun 2020 18:49:57: 14000000 INFO @ Sun, 21 Jun 2020 18:50:00: 10000000 INFO @ Sun, 21 Jun 2020 18:50:00: 6000000 INFO @ Sun, 21 Jun 2020 18:50:06: 15000000 INFO @ Sun, 21 Jun 2020 18:50:08: 7000000 INFO @ Sun, 21 Jun 2020 18:50:08: 11000000 INFO @ Sun, 21 Jun 2020 18:50:14: 16000000 INFO @ Sun, 21 Jun 2020 18:50:16: 8000000 INFO @ Sun, 21 Jun 2020 18:50:16: 12000000 INFO @ Sun, 21 Jun 2020 18:50:22: 17000000 INFO @ Sun, 21 Jun 2020 18:50:23: 9000000 INFO @ Sun, 21 Jun 2020 18:50:24: 13000000 INFO @ Sun, 21 Jun 2020 18:50:30: 18000000 INFO @ Sun, 21 Jun 2020 18:50:30: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:50:30: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:50:30: #1 total tags in treatment: 18093299 INFO @ Sun, 21 Jun 2020 18:50:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:50:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:50:31: #1 tags after filtering in treatment: 18093209 INFO @ Sun, 21 Jun 2020 18:50:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:50:31: #1 finished! INFO @ Sun, 21 Jun 2020 18:50:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:50:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:50:31: 10000000 INFO @ Sun, 21 Jun 2020 18:50:32: 14000000 INFO @ Sun, 21 Jun 2020 18:50:32: #2 number of paired peaks: 1559 INFO @ Sun, 21 Jun 2020 18:50:32: start model_add_line... INFO @ Sun, 21 Jun 2020 18:50:33: start X-correlation... INFO @ Sun, 21 Jun 2020 18:50:33: end of X-cor INFO @ Sun, 21 Jun 2020 18:50:33: #2 finished! INFO @ Sun, 21 Jun 2020 18:50:33: #2 predicted fragment length is 120 bps INFO @ Sun, 21 Jun 2020 18:50:33: #2 alternative fragment length(s) may be 4,120 bps INFO @ Sun, 21 Jun 2020 18:50:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.05_model.r WARNING @ Sun, 21 Jun 2020 18:50:33: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:50:33: #2 You may need to consider one of the other alternative d(s): 4,120 WARNING @ Sun, 21 Jun 2020 18:50:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:50:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:50:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:50:39: 11000000 INFO @ Sun, 21 Jun 2020 18:50:40: 15000000 INFO @ Sun, 21 Jun 2020 18:50:47: 12000000 INFO @ Sun, 21 Jun 2020 18:50:48: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:50:56: 13000000 INFO @ Sun, 21 Jun 2020 18:50:56: 17000000 INFO @ Sun, 21 Jun 2020 18:51:04: 18000000 INFO @ Sun, 21 Jun 2020 18:51:04: 14000000 INFO @ Sun, 21 Jun 2020 18:51:05: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:51:05: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:51:05: #1 total tags in treatment: 18093299 INFO @ Sun, 21 Jun 2020 18:51:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:51:05: #1 tags after filtering in treatment: 18093209 INFO @ Sun, 21 Jun 2020 18:51:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:07: #2 number of paired peaks: 1559 INFO @ Sun, 21 Jun 2020 18:51:07: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:07: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:07: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:07: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:07: #2 predicted fragment length is 120 bps INFO @ Sun, 21 Jun 2020 18:51:07: #2 alternative fragment length(s) may be 4,120 bps INFO @ Sun, 21 Jun 2020 18:51:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.10_model.r WARNING @ Sun, 21 Jun 2020 18:51:07: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:51:07: #2 You may need to consider one of the other alternative d(s): 4,120 WARNING @ Sun, 21 Jun 2020 18:51:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:51:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:12: 15000000 INFO @ Sun, 21 Jun 2020 18:51:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:51:20: 16000000 INFO @ Sun, 21 Jun 2020 18:51:28: 17000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:51:35: 18000000 INFO @ Sun, 21 Jun 2020 18:51:36: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:51:36: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:51:36: #1 total tags in treatment: 18093299 INFO @ Sun, 21 Jun 2020 18:51:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:51:36: #1 tags after filtering in treatment: 18093209 INFO @ Sun, 21 Jun 2020 18:51:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:36: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.05_summits.bed INFO @ Sun, 21 Jun 2020 18:51:37: Done! INFO @ Sun, 21 Jun 2020 18:51:38: #2 number of paired peaks: 1559 INFO @ Sun, 21 Jun 2020 18:51:38: start model_add_line... pass1 - making usageList (632 chroms): 2 millis pass2 - checking and writing primary data (3896 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:51:38: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:38: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:38: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:38: #2 predicted fragment length is 120 bps INFO @ Sun, 21 Jun 2020 18:51:38: #2 alternative fragment length(s) may be 4,120 bps INFO @ Sun, 21 Jun 2020 18:51:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.20_model.r WARNING @ Sun, 21 Jun 2020 18:51:38: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:51:38: #2 You may need to consider one of the other alternative d(s): 4,120 WARNING @ Sun, 21 Jun 2020 18:51:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:51:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.10_summits.bed INFO @ Sun, 21 Jun 2020 18:52:08: Done! pass1 - making usageList (561 chroms): 1 millis pass2 - checking and writing primary data (2795 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:52:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422636/SRX2422636.20_summits.bed INFO @ Sun, 21 Jun 2020 18:52:38: Done! pass1 - making usageList (473 chroms): 1 millis pass2 - checking and writing primary data (1844 records, 4 fields): 16 millis CompletedMACS2peakCalling