Job ID = 6527513 SRX = SRX041398 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:28:37 prefetch.2.10.7: 1) Downloading 'SRR099133'... 2020-06-29T12:28:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:30:26 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:30:27 prefetch.2.10.7: 'SRR099133' is valid 2020-06-29T12:30:27 prefetch.2.10.7: 1) 'SRR099133' was downloaded successfully Read 21964308 spots for SRR099133/SRR099133.sra Written 21964308 spots for SRR099133/SRR099133.sra 2020-06-29T12:31:52 prefetch.2.10.7: 1) Downloading 'SRR099134'... 2020-06-29T12:31:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:34:15 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:34:15 prefetch.2.10.7: 1) 'SRR099134' was downloaded successfully Read 25080217 spots for SRR099134/SRR099134.sra Written 25080217 spots for SRR099134/SRR099134.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: 00:14:30 47044525 reads; of these: 47044525 (100.00%) were unpaired; of these: 2100847 (4.47%) aligned 0 times 35949389 (76.42%) aligned exactly 1 time 8994289 (19.12%) aligned >1 times 95.53% overall alignment rate Time searching: 00:14:30 Overall time: 00:14:30 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] 29036486 / 44943678 = 0.6461 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 22:08:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.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 22:08:40: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:08:40: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:08:45: 1000000 INFO @ Mon, 29 Jun 2020 22:08:50: 2000000 INFO @ Mon, 29 Jun 2020 22:08:55: 3000000 INFO @ Mon, 29 Jun 2020 22:08:59: 4000000 INFO @ Mon, 29 Jun 2020 22:09:04: 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 @ Mon, 29 Jun 2020 22:09:09: 6000000 INFO @ Mon, 29 Jun 2020 22:09:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.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 22:09:10: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:09:10: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:09:14: 7000000 INFO @ Mon, 29 Jun 2020 22:09:16: 1000000 INFO @ Mon, 29 Jun 2020 22:09:19: 8000000 INFO @ Mon, 29 Jun 2020 22:09:20: 2000000 INFO @ Mon, 29 Jun 2020 22:09:24: 9000000 INFO @ Mon, 29 Jun 2020 22:09:25: 3000000 INFO @ Mon, 29 Jun 2020 22:09:30: 10000000 INFO @ Mon, 29 Jun 2020 22:09:30: 4000000 INFO @ Mon, 29 Jun 2020 22:09:35: 5000000 INFO @ Mon, 29 Jun 2020 22:09:36: 11000000 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 22:09:40: 6000000 INFO @ Mon, 29 Jun 2020 22:09:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.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 22:09:40: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:09:40: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:09:42: 12000000 INFO @ Mon, 29 Jun 2020 22:09:45: 7000000 INFO @ Mon, 29 Jun 2020 22:09:46: 1000000 INFO @ Mon, 29 Jun 2020 22:09:48: 13000000 INFO @ Mon, 29 Jun 2020 22:09:50: 8000000 INFO @ Mon, 29 Jun 2020 22:09:52: 2000000 INFO @ Mon, 29 Jun 2020 22:09:54: 14000000 INFO @ Mon, 29 Jun 2020 22:09:55: 9000000 INFO @ Mon, 29 Jun 2020 22:09:59: 3000000 INFO @ Mon, 29 Jun 2020 22:10:00: 10000000 INFO @ Mon, 29 Jun 2020 22:10:01: 15000000 INFO @ Mon, 29 Jun 2020 22:10:05: 4000000 INFO @ Mon, 29 Jun 2020 22:10:05: 11000000 INFO @ Mon, 29 Jun 2020 22:10:07: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:10:07: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:10:07: #1 total tags in treatment: 15907192 INFO @ Mon, 29 Jun 2020 22:10:07: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:10:07: #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 22:10:07: #1 tags after filtering in treatment: 15907192 INFO @ Mon, 29 Jun 2020 22:10:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:10:07: #1 finished! INFO @ Mon, 29 Jun 2020 22:10:07: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:10:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:10:08: #2 number of paired peaks: 410 WARNING @ Mon, 29 Jun 2020 22:10:08: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Mon, 29 Jun 2020 22:10:08: start model_add_line... INFO @ Mon, 29 Jun 2020 22:10:08: start X-correlation... INFO @ Mon, 29 Jun 2020 22:10:08: end of X-cor INFO @ Mon, 29 Jun 2020 22:10:08: #2 finished! INFO @ Mon, 29 Jun 2020 22:10:08: #2 predicted fragment length is 33 bps INFO @ Mon, 29 Jun 2020 22:10:08: #2 alternative fragment length(s) may be 33 bps INFO @ Mon, 29 Jun 2020 22:10:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.05_model.r WARNING @ Mon, 29 Jun 2020 22:10:08: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:10:08: #2 You may need to consider one of the other alternative d(s): 33 WARNING @ Mon, 29 Jun 2020 22:10:08: #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 22:10:08: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:10:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:10:10: 12000000 INFO @ Mon, 29 Jun 2020 22:10:11: 5000000 INFO @ Mon, 29 Jun 2020 22:10:15: 13000000 INFO @ Mon, 29 Jun 2020 22:10:17: 6000000 INFO @ Mon, 29 Jun 2020 22:10:20: 14000000 INFO @ Mon, 29 Jun 2020 22:10:23: 7000000 INFO @ Mon, 29 Jun 2020 22:10:25: 15000000 INFO @ Mon, 29 Jun 2020 22:10:29: 8000000 INFO @ Mon, 29 Jun 2020 22:10:30: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:10:30: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:10:30: #1 total tags in treatment: 15907192 INFO @ Mon, 29 Jun 2020 22:10:30: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:10:30: #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 22:10:31: #1 tags after filtering in treatment: 15907192 INFO @ Mon, 29 Jun 2020 22:10:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:10:31: #1 finished! INFO @ Mon, 29 Jun 2020 22:10:31: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:10:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:10:32: #2 number of paired peaks: 410 WARNING @ Mon, 29 Jun 2020 22:10:32: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Mon, 29 Jun 2020 22:10:32: start model_add_line... INFO @ Mon, 29 Jun 2020 22:10:32: start X-correlation... INFO @ Mon, 29 Jun 2020 22:10:32: end of X-cor INFO @ Mon, 29 Jun 2020 22:10:32: #2 finished! INFO @ Mon, 29 Jun 2020 22:10:32: #2 predicted fragment length is 33 bps INFO @ Mon, 29 Jun 2020 22:10:32: #2 alternative fragment length(s) may be 33 bps INFO @ Mon, 29 Jun 2020 22:10:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.10_model.r WARNING @ Mon, 29 Jun 2020 22:10:32: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:10:32: #2 You may need to consider one of the other alternative d(s): 33 WARNING @ Mon, 29 Jun 2020 22:10:32: #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 22:10:32: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:10:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:10:36: 9000000 INFO @ Mon, 29 Jun 2020 22:10:36: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:10:42: 10000000 INFO @ Mon, 29 Jun 2020 22:10:48: 11000000 INFO @ Mon, 29 Jun 2020 22:10:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:10:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:10:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.05_summits.bed INFO @ Mon, 29 Jun 2020 22:10:51: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3425 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:10:54: 12000000 INFO @ Mon, 29 Jun 2020 22:10:59: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:11:01: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:11:07: 14000000 INFO @ Mon, 29 Jun 2020 22:11:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:11:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:11:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.10_summits.bed INFO @ Mon, 29 Jun 2020 22:11:14: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1702 records, 4 fields): 5 millis INFO @ Mon, 29 Jun 2020 22:11:14: 15000000 CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:11:20: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:11:20: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:11:20: #1 total tags in treatment: 15907192 INFO @ Mon, 29 Jun 2020 22:11:20: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:11:20: #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 22:11:21: #1 tags after filtering in treatment: 15907192 INFO @ Mon, 29 Jun 2020 22:11:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:11:21: #1 finished! INFO @ Mon, 29 Jun 2020 22:11:21: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:11:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:11:22: #2 number of paired peaks: 410 WARNING @ Mon, 29 Jun 2020 22:11:22: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Mon, 29 Jun 2020 22:11:22: start model_add_line... INFO @ Mon, 29 Jun 2020 22:11:22: start X-correlation... INFO @ Mon, 29 Jun 2020 22:11:22: end of X-cor INFO @ Mon, 29 Jun 2020 22:11:22: #2 finished! INFO @ Mon, 29 Jun 2020 22:11:22: #2 predicted fragment length is 33 bps INFO @ Mon, 29 Jun 2020 22:11:22: #2 alternative fragment length(s) may be 33 bps INFO @ Mon, 29 Jun 2020 22:11:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.20_model.r WARNING @ Mon, 29 Jun 2020 22:11:22: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:11:22: #2 You may need to consider one of the other alternative d(s): 33 WARNING @ Mon, 29 Jun 2020 22:11:22: #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 22:11:22: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:11:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:11:49: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:12:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:12:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:12:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX041398/SRX041398.20_summits.bed INFO @ Mon, 29 Jun 2020 22:12:05: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1070 records, 4 fields): 70 millis CompletedMACS2peakCalling