Job ID = 6627526 SRX = SRX8521397 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T02:50:26 prefetch.2.10.7: 1) Downloading 'SRR11978330'... 2020-07-14T02:50:26 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:51:44 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:51:45 prefetch.2.10.7: 'SRR11978330' is valid 2020-07-14T02:51:45 prefetch.2.10.7: 1) 'SRR11978330' was downloaded successfully 2020-07-14T02:51:45 prefetch.2.10.7: 'SRR11978330' has 0 unresolved dependencies Read 12660768 spots for SRR11978330/SRR11978330.sra Written 12660768 spots for SRR11978330/SRR11978330.sra 2020-07-14T02:52:47 prefetch.2.10.7: 1) Downloading 'SRR11978331'... 2020-07-14T02:52:47 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:54:49 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:54:50 prefetch.2.10.7: 'SRR11978331' is valid 2020-07-14T02:54:50 prefetch.2.10.7: 1) 'SRR11978331' was downloaded successfully 2020-07-14T02:54:50 prefetch.2.10.7: 'SRR11978331' has 0 unresolved dependencies Read 12640514 spots for SRR11978331/SRR11978331.sra Written 12640514 spots for SRR11978331/SRR11978331.sra 2020-07-14T02:55:52 prefetch.2.10.7: 1) Downloading 'SRR11978332'... 2020-07-14T02:55:52 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:57:28 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:57:29 prefetch.2.10.7: 'SRR11978332' is valid 2020-07-14T02:57:29 prefetch.2.10.7: 1) 'SRR11978332' was downloaded successfully 2020-07-14T02:57:29 prefetch.2.10.7: 'SRR11978332' has 0 unresolved dependencies Read 12822116 spots for SRR11978332/SRR11978332.sra Written 12822116 spots for SRR11978332/SRR11978332.sra 2020-07-14T02:58:42 prefetch.2.10.7: 1) Downloading 'SRR11978333'... 2020-07-14T02:58:42 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:00:13 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:00:13 prefetch.2.10.7: 'SRR11978333' is valid 2020-07-14T03:00:13 prefetch.2.10.7: 1) 'SRR11978333' was downloaded successfully 2020-07-14T03:00:13 prefetch.2.10.7: 'SRR11978333' has 0 unresolved dependencies Read 12682583 spots for SRR11978333/SRR11978333.sra Written 12682583 spots for SRR11978333/SRR11978333.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627728 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:53 50805981 reads; of these: 50805981 (100.00%) were unpaired; of these: 40065718 (78.86%) aligned 0 times 7962932 (15.67%) aligned exactly 1 time 2777331 (5.47%) aligned >1 times 21.14% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 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] 1903284 / 10740263 = 0.1772 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, 14 Jul 2020 12:13:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.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, 14 Jul 2020 12:13:35: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:13:35: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:13:42: 1000000 INFO @ Tue, 14 Jul 2020 12:13:49: 2000000 INFO @ Tue, 14 Jul 2020 12:13:55: 3000000 INFO @ Tue, 14 Jul 2020 12:14:02: 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, 14 Jul 2020 12:14:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.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, 14 Jul 2020 12:14:05: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:14:05: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:14:08: 5000000 INFO @ Tue, 14 Jul 2020 12:14:12: 1000000 INFO @ Tue, 14 Jul 2020 12:14:15: 6000000 INFO @ Tue, 14 Jul 2020 12:14:19: 2000000 INFO @ Tue, 14 Jul 2020 12:14:22: 7000000 INFO @ Tue, 14 Jul 2020 12:14:26: 3000000 INFO @ Tue, 14 Jul 2020 12:14:29: 8000000 BedGraph に変換中... INFO @ Tue, 14 Jul 2020 12:14:33: 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, 14 Jul 2020 12:14:35: #1 tag size is determined as 61 bps INFO @ Tue, 14 Jul 2020 12:14:35: #1 tag size = 61 INFO @ Tue, 14 Jul 2020 12:14:35: #1 total tags in treatment: 8836979 INFO @ Tue, 14 Jul 2020 12:14:35: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:14:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:14:35: #1 tags after filtering in treatment: 8836979 INFO @ Tue, 14 Jul 2020 12:14:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:14:35: #1 finished! INFO @ Tue, 14 Jul 2020 12:14:35: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:14:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:14:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.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, 14 Jul 2020 12:14:35: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:14:35: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:14:36: #2 number of paired peaks: 230 WARNING @ Tue, 14 Jul 2020 12:14:36: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Tue, 14 Jul 2020 12:14:36: start model_add_line... INFO @ Tue, 14 Jul 2020 12:14:36: start X-correlation... INFO @ Tue, 14 Jul 2020 12:14:36: end of X-cor INFO @ Tue, 14 Jul 2020 12:14:36: #2 finished! INFO @ Tue, 14 Jul 2020 12:14:36: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 12:14:36: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 12:14:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.05_model.r WARNING @ Tue, 14 Jul 2020 12:14:36: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:14:36: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 12:14:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:14:36: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:14:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:14:40: 5000000 INFO @ Tue, 14 Jul 2020 12:14:43: 1000000 INFO @ Tue, 14 Jul 2020 12:14:47: 6000000 INFO @ Tue, 14 Jul 2020 12:14:50: 2000000 INFO @ Tue, 14 Jul 2020 12:14:54: 7000000 INFO @ Tue, 14 Jul 2020 12:14:57: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:14:57: 3000000 INFO @ Tue, 14 Jul 2020 12:15:01: 8000000 INFO @ Tue, 14 Jul 2020 12:15:04: 4000000 INFO @ Tue, 14 Jul 2020 12:15:07: #1 tag size is determined as 61 bps INFO @ Tue, 14 Jul 2020 12:15:07: #1 tag size = 61 INFO @ Tue, 14 Jul 2020 12:15:07: #1 total tags in treatment: 8836979 INFO @ Tue, 14 Jul 2020 12:15:07: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:15:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:15:07: #1 tags after filtering in treatment: 8836979 INFO @ Tue, 14 Jul 2020 12:15:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:15:07: #1 finished! INFO @ Tue, 14 Jul 2020 12:15:07: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:15:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:15:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:15:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:15:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.05_summits.bed INFO @ Tue, 14 Jul 2020 12:15:08: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2422 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:15:08: #2 number of paired peaks: 230 WARNING @ Tue, 14 Jul 2020 12:15:08: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Tue, 14 Jul 2020 12:15:08: start model_add_line... INFO @ Tue, 14 Jul 2020 12:15:08: start X-correlation... INFO @ Tue, 14 Jul 2020 12:15:08: end of X-cor INFO @ Tue, 14 Jul 2020 12:15:08: #2 finished! INFO @ Tue, 14 Jul 2020 12:15:08: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 12:15:08: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 12:15:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.10_model.r WARNING @ Tue, 14 Jul 2020 12:15:08: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:15:08: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 12:15:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:15:08: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:15:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:15:11: 5000000 INFO @ Tue, 14 Jul 2020 12:15:18: 6000000 INFO @ Tue, 14 Jul 2020 12:15:24: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:15:29: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:15:31: 8000000 INFO @ Tue, 14 Jul 2020 12:15:36: #1 tag size is determined as 61 bps INFO @ Tue, 14 Jul 2020 12:15:36: #1 tag size = 61 INFO @ Tue, 14 Jul 2020 12:15:36: #1 total tags in treatment: 8836979 INFO @ Tue, 14 Jul 2020 12:15:36: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:15:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:15:36: #1 tags after filtering in treatment: 8836979 INFO @ Tue, 14 Jul 2020 12:15:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:15:36: #1 finished! INFO @ Tue, 14 Jul 2020 12:15:36: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:15:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:15:37: #2 number of paired peaks: 230 WARNING @ Tue, 14 Jul 2020 12:15:37: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Tue, 14 Jul 2020 12:15:37: start model_add_line... INFO @ Tue, 14 Jul 2020 12:15:37: start X-correlation... INFO @ Tue, 14 Jul 2020 12:15:37: end of X-cor INFO @ Tue, 14 Jul 2020 12:15:37: #2 finished! INFO @ Tue, 14 Jul 2020 12:15:37: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 12:15:37: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 12:15:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.20_model.r WARNING @ Tue, 14 Jul 2020 12:15:37: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:15:37: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 12:15:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:15:37: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:15:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:15:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:15:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:15:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.10_summits.bed INFO @ Tue, 14 Jul 2020 12:15:39: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1008 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:15:57: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:16:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:16:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:16:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521397/SRX8521397.20_summits.bed INFO @ Tue, 14 Jul 2020 12:16:07: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (232 records, 4 fields): 2 millis CompletedMACS2peakCalling