Job ID = 6626641 SRX = SRX7351004 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 18643918 spots for SRR10673634/SRR10673634.sra Written 18643918 spots for SRR10673634/SRR10673634.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626778 ("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: 00:06:36 18643918 reads; of these: 18643918 (100.00%) were unpaired; of these: 668872 (3.59%) aligned 0 times 14131202 (75.80%) aligned exactly 1 time 3843844 (20.62%) aligned >1 times 96.41% overall alignment rate Time searching: 00:06:36 Overall time: 00:06:36 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] 2014956 / 17975046 = 0.1121 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 08:18:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.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 08:18:07: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:18:07: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:18:13: 1000000 INFO @ Tue, 14 Jul 2020 08:18:18: 2000000 INFO @ Tue, 14 Jul 2020 08:18:24: 3000000 INFO @ Tue, 14 Jul 2020 08:18:29: 4000000 INFO @ Tue, 14 Jul 2020 08:18:35: 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 @ Tue, 14 Jul 2020 08:18:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.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 08:18:37: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:18:37: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:18:40: 6000000 INFO @ Tue, 14 Jul 2020 08:18:42: 1000000 INFO @ Tue, 14 Jul 2020 08:18:46: 7000000 INFO @ Tue, 14 Jul 2020 08:18:48: 2000000 INFO @ Tue, 14 Jul 2020 08:18:52: 8000000 INFO @ Tue, 14 Jul 2020 08:18:54: 3000000 INFO @ Tue, 14 Jul 2020 08:18:57: 9000000 INFO @ Tue, 14 Jul 2020 08:18:59: 4000000 INFO @ Tue, 14 Jul 2020 08:19:03: 10000000 INFO @ Tue, 14 Jul 2020 08:19:05: 5000000 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, 14 Jul 2020 08:19:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.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 08:19:07: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:19:07: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:19:08: 11000000 INFO @ Tue, 14 Jul 2020 08:19:10: 6000000 INFO @ Tue, 14 Jul 2020 08:19:13: 1000000 INFO @ Tue, 14 Jul 2020 08:19:14: 12000000 INFO @ Tue, 14 Jul 2020 08:19:16: 7000000 INFO @ Tue, 14 Jul 2020 08:19:20: 2000000 INFO @ Tue, 14 Jul 2020 08:19:20: 13000000 INFO @ Tue, 14 Jul 2020 08:19:22: 8000000 INFO @ Tue, 14 Jul 2020 08:19:26: 3000000 INFO @ Tue, 14 Jul 2020 08:19:26: 14000000 INFO @ Tue, 14 Jul 2020 08:19:28: 9000000 INFO @ Tue, 14 Jul 2020 08:19:31: 4000000 INFO @ Tue, 14 Jul 2020 08:19:32: 15000000 INFO @ Tue, 14 Jul 2020 08:19:34: 10000000 INFO @ Tue, 14 Jul 2020 08:19:37: 5000000 INFO @ Tue, 14 Jul 2020 08:19:38: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:19:38: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:19:38: #1 total tags in treatment: 15960090 INFO @ Tue, 14 Jul 2020 08:19:38: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:19:38: #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 08:19:38: #1 tags after filtering in treatment: 15960090 INFO @ Tue, 14 Jul 2020 08:19:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:19:38: #1 finished! INFO @ Tue, 14 Jul 2020 08:19:38: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:19:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:19:39: #2 number of paired peaks: 962 WARNING @ Tue, 14 Jul 2020 08:19:39: Fewer paired peaks (962) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 962 pairs to build model! INFO @ Tue, 14 Jul 2020 08:19:39: start model_add_line... INFO @ Tue, 14 Jul 2020 08:19:39: start X-correlation... INFO @ Tue, 14 Jul 2020 08:19:39: end of X-cor INFO @ Tue, 14 Jul 2020 08:19:39: #2 finished! INFO @ Tue, 14 Jul 2020 08:19:39: #2 predicted fragment length is 89 bps INFO @ Tue, 14 Jul 2020 08:19:39: #2 alternative fragment length(s) may be 4,89 bps INFO @ Tue, 14 Jul 2020 08:19:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.05_model.r WARNING @ Tue, 14 Jul 2020 08:19:39: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:19:39: #2 You may need to consider one of the other alternative d(s): 4,89 WARNING @ Tue, 14 Jul 2020 08:19:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:19:39: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:19:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:19:39: 11000000 INFO @ Tue, 14 Jul 2020 08:19:43: 6000000 INFO @ Tue, 14 Jul 2020 08:19:45: 12000000 INFO @ Tue, 14 Jul 2020 08:19:48: 7000000 INFO @ Tue, 14 Jul 2020 08:19:51: 13000000 INFO @ Tue, 14 Jul 2020 08:19:54: 8000000 INFO @ Tue, 14 Jul 2020 08:19:57: 14000000 INFO @ Tue, 14 Jul 2020 08:20:00: 9000000 INFO @ Tue, 14 Jul 2020 08:20:02: 15000000 INFO @ Tue, 14 Jul 2020 08:20:06: 10000000 INFO @ Tue, 14 Jul 2020 08:20:08: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:20:08: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:20:08: #1 total tags in treatment: 15960090 INFO @ Tue, 14 Jul 2020 08:20:08: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:20:08: #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 08:20:08: #1 tags after filtering in treatment: 15960090 INFO @ Tue, 14 Jul 2020 08:20:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:20:08: #1 finished! INFO @ Tue, 14 Jul 2020 08:20:08: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:20:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:20:09: #2 number of paired peaks: 962 WARNING @ Tue, 14 Jul 2020 08:20:09: Fewer paired peaks (962) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 962 pairs to build model! INFO @ Tue, 14 Jul 2020 08:20:09: start model_add_line... INFO @ Tue, 14 Jul 2020 08:20:09: start X-correlation... INFO @ Tue, 14 Jul 2020 08:20:09: end of X-cor INFO @ Tue, 14 Jul 2020 08:20:09: #2 finished! INFO @ Tue, 14 Jul 2020 08:20:09: #2 predicted fragment length is 89 bps INFO @ Tue, 14 Jul 2020 08:20:09: #2 alternative fragment length(s) may be 4,89 bps INFO @ Tue, 14 Jul 2020 08:20:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.10_model.r WARNING @ Tue, 14 Jul 2020 08:20:09: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:20:09: #2 You may need to consider one of the other alternative d(s): 4,89 WARNING @ Tue, 14 Jul 2020 08:20:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:20:09: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:20:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:20:11: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:20:11: 11000000 INFO @ Tue, 14 Jul 2020 08:20:17: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:20:22: 13000000 INFO @ Tue, 14 Jul 2020 08:20:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:20:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:20:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.05_summits.bed INFO @ Tue, 14 Jul 2020 08:20:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7543 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:20:28: 14000000 INFO @ Tue, 14 Jul 2020 08:20:33: 15000000 INFO @ Tue, 14 Jul 2020 08:20:38: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:20:38: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:20:38: #1 total tags in treatment: 15960090 INFO @ Tue, 14 Jul 2020 08:20:38: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:20:38: #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 08:20:39: #1 tags after filtering in treatment: 15960090 INFO @ Tue, 14 Jul 2020 08:20:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:20:39: #1 finished! INFO @ Tue, 14 Jul 2020 08:20:39: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:20:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:20:40: #2 number of paired peaks: 962 WARNING @ Tue, 14 Jul 2020 08:20:40: Fewer paired peaks (962) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 962 pairs to build model! INFO @ Tue, 14 Jul 2020 08:20:40: start model_add_line... INFO @ Tue, 14 Jul 2020 08:20:40: start X-correlation... INFO @ Tue, 14 Jul 2020 08:20:40: end of X-cor INFO @ Tue, 14 Jul 2020 08:20:40: #2 finished! INFO @ Tue, 14 Jul 2020 08:20:40: #2 predicted fragment length is 89 bps INFO @ Tue, 14 Jul 2020 08:20:40: #2 alternative fragment length(s) may be 4,89 bps INFO @ Tue, 14 Jul 2020 08:20:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.20_model.r WARNING @ Tue, 14 Jul 2020 08:20:40: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:20:40: #2 You may need to consider one of the other alternative d(s): 4,89 WARNING @ Tue, 14 Jul 2020 08:20:40: #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 08:20:40: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:20:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:20:41: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:20:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:20:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:20:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.10_summits.bed INFO @ Tue, 14 Jul 2020 08:20:57: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3792 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:21:11: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:21:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:21:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:21:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351004/SRX7351004.20_summits.bed INFO @ Tue, 14 Jul 2020 08:21:26: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1298 records, 4 fields): 3 millis CompletedMACS2peakCalling