Job ID = 12265296 SRX = SRX5010755 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 33979005 spots for SRR8191180/SRR8191180.sra Written 33979005 spots for SRR8191180/SRR8191180.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265444 ("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: 00:09:05 33979005 reads; of these: 33979005 (100.00%) were unpaired; of these: 1033740 (3.04%) aligned 0 times 15524776 (45.69%) aligned exactly 1 time 17420489 (51.27%) aligned >1 times 96.96% overall alignment rate Time searching: 00:09:06 Overall time: 00:09:06 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 16 files... [bam_rmdupse_core] 19660178 / 32945265 = 0.5968 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:42:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.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 @ Sat, 03 Apr 2021 06:42:57: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:42:57: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:43:02: 1000000 INFO @ Sat, 03 Apr 2021 06:43:07: 2000000 INFO @ Sat, 03 Apr 2021 06:43:13: 3000000 INFO @ Sat, 03 Apr 2021 06:43:17: 4000000 INFO @ Sat, 03 Apr 2021 06:43:22: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:43:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.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 @ Sat, 03 Apr 2021 06:43:27: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:43:27: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:43:28: 6000000 INFO @ Sat, 03 Apr 2021 06:43:32: 1000000 INFO @ Sat, 03 Apr 2021 06:43:33: 7000000 INFO @ Sat, 03 Apr 2021 06:43:37: 2000000 INFO @ Sat, 03 Apr 2021 06:43:38: 8000000 INFO @ Sat, 03 Apr 2021 06:43:43: 3000000 INFO @ Sat, 03 Apr 2021 06:43:43: 9000000 INFO @ Sat, 03 Apr 2021 06:43:48: 4000000 INFO @ Sat, 03 Apr 2021 06:43:48: 10000000 INFO @ Sat, 03 Apr 2021 06:43:54: 5000000 INFO @ Sat, 03 Apr 2021 06:43:54: 11000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:43:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.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 @ Sat, 03 Apr 2021 06:43:57: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:43:57: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:43:59: 6000000 INFO @ Sat, 03 Apr 2021 06:43:59: 12000000 INFO @ Sat, 03 Apr 2021 06:44:02: 1000000 INFO @ Sat, 03 Apr 2021 06:44:05: 7000000 INFO @ Sat, 03 Apr 2021 06:44:05: 13000000 INFO @ Sat, 03 Apr 2021 06:44:06: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:44:06: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:44:06: #1 total tags in treatment: 13285087 INFO @ Sat, 03 Apr 2021 06:44:06: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:44:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:44:07: #1 tags after filtering in treatment: 13285087 INFO @ Sat, 03 Apr 2021 06:44:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:44:07: #1 finished! INFO @ Sat, 03 Apr 2021 06:44:07: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:44:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:44:07: 2000000 INFO @ Sat, 03 Apr 2021 06:44:07: #2 number of paired peaks: 369 WARNING @ Sat, 03 Apr 2021 06:44:07: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Sat, 03 Apr 2021 06:44:07: start model_add_line... INFO @ Sat, 03 Apr 2021 06:44:08: start X-correlation... INFO @ Sat, 03 Apr 2021 06:44:08: end of X-cor INFO @ Sat, 03 Apr 2021 06:44:08: #2 finished! INFO @ Sat, 03 Apr 2021 06:44:08: #2 predicted fragment length is 67 bps INFO @ Sat, 03 Apr 2021 06:44:08: #2 alternative fragment length(s) may be 67 bps INFO @ Sat, 03 Apr 2021 06:44:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.05_model.r WARNING @ Sat, 03 Apr 2021 06:44:08: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:44:08: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Sat, 03 Apr 2021 06:44:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:44:08: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:44:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:44:10: 8000000 INFO @ Sat, 03 Apr 2021 06:44:12: 3000000 INFO @ Sat, 03 Apr 2021 06:44:14: 9000000 INFO @ Sat, 03 Apr 2021 06:44:16: 4000000 INFO @ Sat, 03 Apr 2021 06:44:19: 10000000 INFO @ Sat, 03 Apr 2021 06:44:21: 5000000 INFO @ Sat, 03 Apr 2021 06:44:24: 11000000 INFO @ Sat, 03 Apr 2021 06:44:26: 6000000 INFO @ Sat, 03 Apr 2021 06:44:29: 12000000 INFO @ Sat, 03 Apr 2021 06:44:32: 7000000 INFO @ Sat, 03 Apr 2021 06:44:32: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:44:35: 13000000 INFO @ Sat, 03 Apr 2021 06:44:37: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:44:37: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:44:37: #1 total tags in treatment: 13285087 INFO @ Sat, 03 Apr 2021 06:44:37: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:44:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:44:37: #1 tags after filtering in treatment: 13285087 INFO @ Sat, 03 Apr 2021 06:44:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:44:37: #1 finished! INFO @ Sat, 03 Apr 2021 06:44:37: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:44:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:44:37: 8000000 INFO @ Sat, 03 Apr 2021 06:44:38: #2 number of paired peaks: 369 WARNING @ Sat, 03 Apr 2021 06:44:38: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Sat, 03 Apr 2021 06:44:38: start model_add_line... INFO @ Sat, 03 Apr 2021 06:44:38: start X-correlation... INFO @ Sat, 03 Apr 2021 06:44:38: end of X-cor INFO @ Sat, 03 Apr 2021 06:44:38: #2 finished! INFO @ Sat, 03 Apr 2021 06:44:38: #2 predicted fragment length is 67 bps INFO @ Sat, 03 Apr 2021 06:44:38: #2 alternative fragment length(s) may be 67 bps INFO @ Sat, 03 Apr 2021 06:44:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.10_model.r WARNING @ Sat, 03 Apr 2021 06:44:38: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:44:38: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Sat, 03 Apr 2021 06:44:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:44:38: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:44:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:44:42: 9000000 INFO @ Sat, 03 Apr 2021 06:44:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:44:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:44:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.05_summits.bed INFO @ Sat, 03 Apr 2021 06:44:46: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8276 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:44:47: 10000000 INFO @ Sat, 03 Apr 2021 06:44:52: 11000000 INFO @ Sat, 03 Apr 2021 06:44:57: 12000000 INFO @ Sat, 03 Apr 2021 06:45:02: 13000000 INFO @ Sat, 03 Apr 2021 06:45:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:45:04: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:45:04: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:45:04: #1 total tags in treatment: 13285087 INFO @ Sat, 03 Apr 2021 06:45:04: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:45:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:45:04: #1 tags after filtering in treatment: 13285087 INFO @ Sat, 03 Apr 2021 06:45:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:45:04: #1 finished! INFO @ Sat, 03 Apr 2021 06:45:04: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:45:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:45:05: #2 number of paired peaks: 369 WARNING @ Sat, 03 Apr 2021 06:45:05: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Sat, 03 Apr 2021 06:45:05: start model_add_line... INFO @ Sat, 03 Apr 2021 06:45:05: start X-correlation... INFO @ Sat, 03 Apr 2021 06:45:05: end of X-cor INFO @ Sat, 03 Apr 2021 06:45:05: #2 finished! INFO @ Sat, 03 Apr 2021 06:45:05: #2 predicted fragment length is 67 bps INFO @ Sat, 03 Apr 2021 06:45:05: #2 alternative fragment length(s) may be 67 bps INFO @ Sat, 03 Apr 2021 06:45:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.20_model.r WARNING @ Sat, 03 Apr 2021 06:45:05: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:45:05: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Sat, 03 Apr 2021 06:45:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:45:05: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:45:05: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:45:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:45:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:45:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.10_summits.bed INFO @ Sat, 03 Apr 2021 06:45:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4075 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:45:29: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:45:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:45:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:45:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010755/SRX5010755.20_summits.bed INFO @ Sat, 03 Apr 2021 06:45:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1223 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。