Job ID = 6528274 SRX = SRX495778 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:55:43 prefetch.2.10.7: 1) Downloading 'SRR1199476'... 2020-06-29T14:55:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:57:24 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:57:24 prefetch.2.10.7: 1) 'SRR1199476' was downloaded successfully Read 17643933 spots for SRR1199476/SRR1199476.sra Written 17643933 spots for SRR1199476/SRR1199476.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: 00:07:08 17643933 reads; of these: 17643933 (100.00%) were unpaired; of these: 997771 (5.66%) aligned 0 times 11037562 (62.56%) aligned exactly 1 time 5608600 (31.79%) aligned >1 times 94.34% overall alignment rate Time searching: 00:07:08 Overall time: 00:07:08 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 8 files... [bam_rmdupse_core] 3432734 / 16646162 = 0.2062 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 00:15:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.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 00:15:17: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:15:17: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:15:23: 1000000 INFO @ Tue, 30 Jun 2020 00:15:28: 2000000 INFO @ Tue, 30 Jun 2020 00:15:34: 3000000 INFO @ Tue, 30 Jun 2020 00:15:40: 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 @ Tue, 30 Jun 2020 00:15:46: 5000000 INFO @ Tue, 30 Jun 2020 00:15:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.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 00:15:47: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:15:47: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:15:52: 6000000 INFO @ Tue, 30 Jun 2020 00:15:53: 1000000 INFO @ Tue, 30 Jun 2020 00:15:58: 7000000 INFO @ Tue, 30 Jun 2020 00:16:00: 2000000 INFO @ Tue, 30 Jun 2020 00:16:05: 8000000 INFO @ Tue, 30 Jun 2020 00:16:06: 3000000 INFO @ Tue, 30 Jun 2020 00:16:11: 9000000 INFO @ Tue, 30 Jun 2020 00:16:13: 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 00:16:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.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 00:16:17: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:16:17: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:16:17: 10000000 INFO @ Tue, 30 Jun 2020 00:16:19: 5000000 INFO @ Tue, 30 Jun 2020 00:16:24: 11000000 INFO @ Tue, 30 Jun 2020 00:16:24: 1000000 INFO @ Tue, 30 Jun 2020 00:16:25: 6000000 INFO @ Tue, 30 Jun 2020 00:16:30: 12000000 INFO @ Tue, 30 Jun 2020 00:16:30: 2000000 INFO @ Tue, 30 Jun 2020 00:16:32: 7000000 INFO @ Tue, 30 Jun 2020 00:16:36: 13000000 INFO @ Tue, 30 Jun 2020 00:16:37: 3000000 INFO @ Tue, 30 Jun 2020 00:16:37: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:16:37: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:16:37: #1 total tags in treatment: 13213428 INFO @ Tue, 30 Jun 2020 00:16:37: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:16:37: #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 00:16:38: #1 tags after filtering in treatment: 13213428 INFO @ Tue, 30 Jun 2020 00:16:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:16:38: #1 finished! INFO @ Tue, 30 Jun 2020 00:16:38: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:16:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:16:38: 8000000 INFO @ Tue, 30 Jun 2020 00:16:39: #2 number of paired peaks: 111 WARNING @ Tue, 30 Jun 2020 00:16:39: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Tue, 30 Jun 2020 00:16:39: start model_add_line... INFO @ Tue, 30 Jun 2020 00:16:39: start X-correlation... INFO @ Tue, 30 Jun 2020 00:16:39: end of X-cor INFO @ Tue, 30 Jun 2020 00:16:39: #2 finished! INFO @ Tue, 30 Jun 2020 00:16:39: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 00:16:39: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 30 Jun 2020 00:16:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.05_model.r WARNING @ Tue, 30 Jun 2020 00:16:39: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:16:39: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 30 Jun 2020 00:16:39: #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 00:16:39: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:16:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:16:43: 4000000 INFO @ Tue, 30 Jun 2020 00:16:44: 9000000 INFO @ Tue, 30 Jun 2020 00:16:50: 10000000 INFO @ Tue, 30 Jun 2020 00:16:50: 5000000 INFO @ Tue, 30 Jun 2020 00:16:55: 11000000 INFO @ Tue, 30 Jun 2020 00:16:57: 6000000 INFO @ Tue, 30 Jun 2020 00:17:01: 12000000 INFO @ Tue, 30 Jun 2020 00:17:02: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:17:03: 7000000 INFO @ Tue, 30 Jun 2020 00:17:07: 13000000 INFO @ Tue, 30 Jun 2020 00:17:08: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:17:08: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:17:08: #1 total tags in treatment: 13213428 INFO @ Tue, 30 Jun 2020 00:17:08: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:17:08: #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 00:17:08: #1 tags after filtering in treatment: 13213428 INFO @ Tue, 30 Jun 2020 00:17:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:17:08: #1 finished! INFO @ Tue, 30 Jun 2020 00:17:08: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:17:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:17:09: #2 number of paired peaks: 111 WARNING @ Tue, 30 Jun 2020 00:17:09: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Tue, 30 Jun 2020 00:17:09: start model_add_line... INFO @ Tue, 30 Jun 2020 00:17:09: start X-correlation... INFO @ Tue, 30 Jun 2020 00:17:09: end of X-cor INFO @ Tue, 30 Jun 2020 00:17:09: #2 finished! INFO @ Tue, 30 Jun 2020 00:17:09: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 00:17:09: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 30 Jun 2020 00:17:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.10_model.r WARNING @ Tue, 30 Jun 2020 00:17:09: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:17:09: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 30 Jun 2020 00:17:09: #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 00:17:09: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:17:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:17:10: 8000000 INFO @ Tue, 30 Jun 2020 00:17:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:17:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:17:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.05_summits.bed INFO @ Tue, 30 Jun 2020 00:17:14: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1255 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:17:16: 9000000 INFO @ Tue, 30 Jun 2020 00:17:23: 10000000 INFO @ Tue, 30 Jun 2020 00:17:29: 11000000 INFO @ Tue, 30 Jun 2020 00:17:33: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:17:36: 12000000 INFO @ Tue, 30 Jun 2020 00:17:42: 13000000 INFO @ Tue, 30 Jun 2020 00:17:44: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:17:44: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:17:44: #1 total tags in treatment: 13213428 INFO @ Tue, 30 Jun 2020 00:17:44: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:17:44: #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 00:17:44: #1 tags after filtering in treatment: 13213428 INFO @ Tue, 30 Jun 2020 00:17:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:17:44: #1 finished! INFO @ Tue, 30 Jun 2020 00:17:44: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:17:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:17:45: #2 number of paired peaks: 111 WARNING @ Tue, 30 Jun 2020 00:17:45: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Tue, 30 Jun 2020 00:17:45: start model_add_line... INFO @ Tue, 30 Jun 2020 00:17:45: start X-correlation... INFO @ Tue, 30 Jun 2020 00:17:45: end of X-cor INFO @ Tue, 30 Jun 2020 00:17:45: #2 finished! INFO @ Tue, 30 Jun 2020 00:17:45: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 00:17:45: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 30 Jun 2020 00:17:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.20_model.r WARNING @ Tue, 30 Jun 2020 00:17:45: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:17:45: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 30 Jun 2020 00:17:45: #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 00:17:45: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:17:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:17:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:17:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:17:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.10_summits.bed INFO @ Tue, 30 Jun 2020 00:17:45: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (944 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:18:08: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:18:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:18:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:18:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495778/SRX495778.20_summits.bed INFO @ Tue, 30 Jun 2020 00:18:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (448 records, 4 fields): 2 millis CompletedMACS2peakCalling