Job ID = 6455502 SRX = SRX287838 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:07:51 prefetch.2.10.7: 1) Downloading 'SRR870027'... 2020-06-21T10:07:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:10:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:10:34 prefetch.2.10.7: 1) 'SRR870027' was downloaded successfully Read 17133552 spots for SRR870027/SRR870027.sra Written 17133552 spots for SRR870027/SRR870027.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:11 17133552 reads; of these: 17133552 (100.00%) were unpaired; of these: 963581 (5.62%) aligned 0 times 11195750 (65.34%) aligned exactly 1 time 4974221 (29.03%) aligned >1 times 94.38% overall alignment rate Time searching: 00:05:12 Overall time: 00:05:12 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 8 files... [bam_rmdupse_core] 2735416 / 16169971 = 0.1692 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 19:21:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.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 19:21:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:21:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:21:11: 1000000 INFO @ Sun, 21 Jun 2020 19:21:17: 2000000 INFO @ Sun, 21 Jun 2020 19:21:23: 3000000 INFO @ Sun, 21 Jun 2020 19:21:29: 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 19:21:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.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 19:21:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:21:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:21:35: 5000000 INFO @ Sun, 21 Jun 2020 19:21:42: 1000000 INFO @ Sun, 21 Jun 2020 19:21:42: 6000000 INFO @ Sun, 21 Jun 2020 19:21:48: 2000000 INFO @ Sun, 21 Jun 2020 19:21:48: 7000000 INFO @ Sun, 21 Jun 2020 19:21:55: 3000000 INFO @ Sun, 21 Jun 2020 19:21:55: 8000000 INFO @ Sun, 21 Jun 2020 19:22:01: 4000000 INFO @ Sun, 21 Jun 2020 19:22:02: 9000000 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 19:22:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.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 19:22:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:22:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:22:08: 5000000 INFO @ Sun, 21 Jun 2020 19:22:08: 10000000 INFO @ Sun, 21 Jun 2020 19:22:12: 1000000 INFO @ Sun, 21 Jun 2020 19:22:14: 6000000 INFO @ Sun, 21 Jun 2020 19:22:15: 11000000 INFO @ Sun, 21 Jun 2020 19:22:19: 2000000 INFO @ Sun, 21 Jun 2020 19:22:21: 7000000 INFO @ Sun, 21 Jun 2020 19:22:22: 12000000 INFO @ Sun, 21 Jun 2020 19:22:26: 3000000 INFO @ Sun, 21 Jun 2020 19:22:27: 8000000 INFO @ Sun, 21 Jun 2020 19:22:29: 13000000 INFO @ Sun, 21 Jun 2020 19:22:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:22:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:22:32: #1 total tags in treatment: 13434555 INFO @ Sun, 21 Jun 2020 19:22:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:22:32: #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 19:22:32: 4000000 INFO @ Sun, 21 Jun 2020 19:22:32: #1 tags after filtering in treatment: 13434555 INFO @ Sun, 21 Jun 2020 19:22:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:22:32: #1 finished! INFO @ Sun, 21 Jun 2020 19:22:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:22:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:22:33: #2 number of paired peaks: 438 WARNING @ Sun, 21 Jun 2020 19:22:33: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Sun, 21 Jun 2020 19:22:33: start model_add_line... INFO @ Sun, 21 Jun 2020 19:22:33: start X-correlation... INFO @ Sun, 21 Jun 2020 19:22:33: end of X-cor INFO @ Sun, 21 Jun 2020 19:22:33: #2 finished! INFO @ Sun, 21 Jun 2020 19:22:33: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:22:33: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 19:22:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.05_model.r WARNING @ Sun, 21 Jun 2020 19:22:34: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:22:34: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 19:22:34: #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 19:22:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:22:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:22:34: 9000000 INFO @ Sun, 21 Jun 2020 19:22:39: 5000000 INFO @ Sun, 21 Jun 2020 19:22:40: 10000000 INFO @ Sun, 21 Jun 2020 19:22:46: 6000000 INFO @ Sun, 21 Jun 2020 19:22:47: 11000000 INFO @ Sun, 21 Jun 2020 19:22:52: 7000000 INFO @ Sun, 21 Jun 2020 19:22:54: 12000000 INFO @ Sun, 21 Jun 2020 19:22:59: 8000000 INFO @ Sun, 21 Jun 2020 19:23:01: 13000000 INFO @ Sun, 21 Jun 2020 19:23:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:23:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:23:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:23:04: #1 total tags in treatment: 13434555 INFO @ Sun, 21 Jun 2020 19:23:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:23:04: #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 19:23:04: #1 tags after filtering in treatment: 13434555 INFO @ Sun, 21 Jun 2020 19:23:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:23:04: #1 finished! INFO @ Sun, 21 Jun 2020 19:23:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:23:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:23:05: #2 number of paired peaks: 438 WARNING @ Sun, 21 Jun 2020 19:23:05: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Sun, 21 Jun 2020 19:23:05: start model_add_line... INFO @ Sun, 21 Jun 2020 19:23:05: start X-correlation... INFO @ Sun, 21 Jun 2020 19:23:05: end of X-cor INFO @ Sun, 21 Jun 2020 19:23:05: #2 finished! INFO @ Sun, 21 Jun 2020 19:23:05: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:23:05: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 19:23:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.10_model.r WARNING @ Sun, 21 Jun 2020 19:23:05: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:23:05: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 19:23:05: #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 19:23:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:23:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:23:06: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:23:12: 10000000 INFO @ Sun, 21 Jun 2020 19:23:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:23:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:23:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.05_summits.bed INFO @ Sun, 21 Jun 2020 19:23:15: Done! pass1 - making usageList (604 chroms): 1 millis pass2 - checking and writing primary data (2433 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:23:18: 11000000 INFO @ Sun, 21 Jun 2020 19:23:25: 12000000 INFO @ Sun, 21 Jun 2020 19:23:31: 13000000 INFO @ Sun, 21 Jun 2020 19:23:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:23:34: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:23:34: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:23:34: #1 total tags in treatment: 13434555 INFO @ Sun, 21 Jun 2020 19:23:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:23:34: #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 19:23:34: #1 tags after filtering in treatment: 13434555 INFO @ Sun, 21 Jun 2020 19:23:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:23:34: #1 finished! INFO @ Sun, 21 Jun 2020 19:23:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:23:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:23:35: #2 number of paired peaks: 438 WARNING @ Sun, 21 Jun 2020 19:23:35: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Sun, 21 Jun 2020 19:23:35: start model_add_line... INFO @ Sun, 21 Jun 2020 19:23:35: start X-correlation... INFO @ Sun, 21 Jun 2020 19:23:35: end of X-cor INFO @ Sun, 21 Jun 2020 19:23:35: #2 finished! INFO @ Sun, 21 Jun 2020 19:23:35: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:23:35: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 19:23:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.20_model.r WARNING @ Sun, 21 Jun 2020 19:23:35: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:23:35: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 19:23:35: #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 19:23:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:23:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:23:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:23:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:23:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.10_summits.bed INFO @ Sun, 21 Jun 2020 19:23:46: Done! pass1 - making usageList (501 chroms): 1 millis pass2 - checking and writing primary data (1730 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:24:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:24:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:24:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:24:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287838/SRX287838.20_summits.bed INFO @ Sun, 21 Jun 2020 19:24:17: Done! pass1 - making usageList (276 chroms): 1 millis pass2 - checking and writing primary data (565 records, 4 fields): 9 millis CompletedMACS2peakCalling