Job ID = 6529758 SRX = SRX467042 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:09:22 28609687 reads; of these: 28609687 (100.00%) were unpaired; of these: 3218105 (11.25%) aligned 0 times 18483605 (64.61%) aligned exactly 1 time 6907977 (24.15%) aligned >1 times 88.75% overall alignment rate Time searching: 00:09:22 Overall time: 00:09:22 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 12 files... [bam_rmdupse_core] 8989234 / 25391582 = 0.3540 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, 30 Jun 2020 03:02:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.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, 30 Jun 2020 03:02:07: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:02:07: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:02:13: 1000000 INFO @ Tue, 30 Jun 2020 03:02:20: 2000000 INFO @ Tue, 30 Jun 2020 03:02:27: 3000000 INFO @ Tue, 30 Jun 2020 03:02:34: 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, 30 Jun 2020 03:02:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.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, 30 Jun 2020 03:02:37: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:02:37: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:02:41: 5000000 INFO @ Tue, 30 Jun 2020 03:02:44: 1000000 INFO @ Tue, 30 Jun 2020 03:02:49: 6000000 INFO @ Tue, 30 Jun 2020 03:02:52: 2000000 INFO @ Tue, 30 Jun 2020 03:02:56: 7000000 INFO @ Tue, 30 Jun 2020 03:02:59: 3000000 INFO @ Tue, 30 Jun 2020 03:03:04: 8000000 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, 30 Jun 2020 03:03:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.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, 30 Jun 2020 03:03:07: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:03:07: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:03:07: 4000000 INFO @ Tue, 30 Jun 2020 03:03:11: 9000000 INFO @ Tue, 30 Jun 2020 03:03:15: 5000000 INFO @ Tue, 30 Jun 2020 03:03:16: 1000000 INFO @ Tue, 30 Jun 2020 03:03:19: 10000000 INFO @ Tue, 30 Jun 2020 03:03:23: 6000000 INFO @ Tue, 30 Jun 2020 03:03:25: 2000000 INFO @ Tue, 30 Jun 2020 03:03:27: 11000000 INFO @ Tue, 30 Jun 2020 03:03:30: 7000000 INFO @ Tue, 30 Jun 2020 03:03:34: 12000000 INFO @ Tue, 30 Jun 2020 03:03:35: 3000000 INFO @ Tue, 30 Jun 2020 03:03:38: 8000000 INFO @ Tue, 30 Jun 2020 03:03:42: 13000000 INFO @ Tue, 30 Jun 2020 03:03:44: 4000000 INFO @ Tue, 30 Jun 2020 03:03:46: 9000000 INFO @ Tue, 30 Jun 2020 03:03:51: 14000000 INFO @ Tue, 30 Jun 2020 03:03:53: 5000000 INFO @ Tue, 30 Jun 2020 03:03:54: 10000000 INFO @ Tue, 30 Jun 2020 03:03:58: 15000000 INFO @ Tue, 30 Jun 2020 03:04:01: 11000000 INFO @ Tue, 30 Jun 2020 03:04:03: 6000000 INFO @ Tue, 30 Jun 2020 03:04:06: 16000000 INFO @ Tue, 30 Jun 2020 03:04:09: 12000000 INFO @ Tue, 30 Jun 2020 03:04:10: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:04:10: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:04:10: #1 total tags in treatment: 16402348 INFO @ Tue, 30 Jun 2020 03:04:10: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:04:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:04:11: #1 tags after filtering in treatment: 16402341 INFO @ Tue, 30 Jun 2020 03:04:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:04:11: #1 finished! INFO @ Tue, 30 Jun 2020 03:04:11: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:04:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:04:12: #2 number of paired peaks: 302 WARNING @ Tue, 30 Jun 2020 03:04:12: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Tue, 30 Jun 2020 03:04:12: start model_add_line... INFO @ Tue, 30 Jun 2020 03:04:12: start X-correlation... INFO @ Tue, 30 Jun 2020 03:04:12: end of X-cor INFO @ Tue, 30 Jun 2020 03:04:12: #2 finished! INFO @ Tue, 30 Jun 2020 03:04:12: #2 predicted fragment length is 35 bps INFO @ Tue, 30 Jun 2020 03:04:12: #2 alternative fragment length(s) may be 3,12,35,487,552,560,593 bps INFO @ Tue, 30 Jun 2020 03:04:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.05_model.r WARNING @ Tue, 30 Jun 2020 03:04:12: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:04:12: #2 You may need to consider one of the other alternative d(s): 3,12,35,487,552,560,593 WARNING @ Tue, 30 Jun 2020 03:04:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:04:12: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:04:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:04:12: 7000000 INFO @ Tue, 30 Jun 2020 03:04:16: 13000000 INFO @ Tue, 30 Jun 2020 03:04:21: 8000000 INFO @ Tue, 30 Jun 2020 03:04:24: 14000000 INFO @ Tue, 30 Jun 2020 03:04:30: 9000000 INFO @ Tue, 30 Jun 2020 03:04:31: 15000000 INFO @ Tue, 30 Jun 2020 03:04:39: 16000000 INFO @ Tue, 30 Jun 2020 03:04:39: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:04:41: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:04:42: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:04:42: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:04:42: #1 total tags in treatment: 16402348 INFO @ Tue, 30 Jun 2020 03:04:42: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:04:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:04:43: #1 tags after filtering in treatment: 16402341 INFO @ Tue, 30 Jun 2020 03:04:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:04:43: #1 finished! INFO @ Tue, 30 Jun 2020 03:04:43: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:04:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:04:44: #2 number of paired peaks: 302 WARNING @ Tue, 30 Jun 2020 03:04:44: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Tue, 30 Jun 2020 03:04:44: start model_add_line... INFO @ Tue, 30 Jun 2020 03:04:44: start X-correlation... INFO @ Tue, 30 Jun 2020 03:04:44: end of X-cor INFO @ Tue, 30 Jun 2020 03:04:44: #2 finished! INFO @ Tue, 30 Jun 2020 03:04:44: #2 predicted fragment length is 35 bps INFO @ Tue, 30 Jun 2020 03:04:44: #2 alternative fragment length(s) may be 3,12,35,487,552,560,593 bps INFO @ Tue, 30 Jun 2020 03:04:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.10_model.r WARNING @ Tue, 30 Jun 2020 03:04:44: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:04:44: #2 You may need to consider one of the other alternative d(s): 3,12,35,487,552,560,593 WARNING @ Tue, 30 Jun 2020 03:04:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:04:44: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:04:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:04:48: 11000000 INFO @ Tue, 30 Jun 2020 03:04:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:04:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:04:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.05_summits.bed INFO @ Tue, 30 Jun 2020 03:04:56: Done! pass1 - making usageList (463 chroms): 2 millis pass2 - checking and writing primary data (2071 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:04:57: 12000000 INFO @ Tue, 30 Jun 2020 03:05:05: 13000000 INFO @ Tue, 30 Jun 2020 03:05:12: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:05:13: 14000000 INFO @ Tue, 30 Jun 2020 03:05:20: 15000000 INFO @ Tue, 30 Jun 2020 03:05:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:05:27: 16000000 INFO @ Tue, 30 Jun 2020 03:05:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:05:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.10_summits.bed INFO @ Tue, 30 Jun 2020 03:05:28: Done! pass1 - making usageList (386 chroms): 1 millis pass2 - checking and writing primary data (1246 records, 4 fields): 23 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:05:31: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:05:31: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:05:31: #1 total tags in treatment: 16402348 INFO @ Tue, 30 Jun 2020 03:05:31: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:05:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:05:32: #1 tags after filtering in treatment: 16402341 INFO @ Tue, 30 Jun 2020 03:05:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:05:32: #1 finished! INFO @ Tue, 30 Jun 2020 03:05:32: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:05:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:05:33: #2 number of paired peaks: 302 WARNING @ Tue, 30 Jun 2020 03:05:33: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Tue, 30 Jun 2020 03:05:33: start model_add_line... INFO @ Tue, 30 Jun 2020 03:05:33: start X-correlation... INFO @ Tue, 30 Jun 2020 03:05:33: end of X-cor INFO @ Tue, 30 Jun 2020 03:05:33: #2 finished! INFO @ Tue, 30 Jun 2020 03:05:33: #2 predicted fragment length is 35 bps INFO @ Tue, 30 Jun 2020 03:05:33: #2 alternative fragment length(s) may be 3,12,35,487,552,560,593 bps INFO @ Tue, 30 Jun 2020 03:05:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.20_model.r WARNING @ Tue, 30 Jun 2020 03:05:33: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:05:33: #2 You may need to consider one of the other alternative d(s): 3,12,35,487,552,560,593 WARNING @ Tue, 30 Jun 2020 03:05:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:05:33: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:05:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:06:02: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:06:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:06:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:06:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467042/SRX467042.20_summits.bed INFO @ Tue, 30 Jun 2020 03:06:17: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (100 records, 4 fields): 5 millis CompletedMACS2peakCalling