Job ID = 14171797 SRX = SRX9986153 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: 00:03:25 14563117 reads; of these: 14563117 (100.00%) were unpaired; of these: 3405922 (23.39%) aligned 0 times 8592560 (59.00%) aligned exactly 1 time 2564635 (17.61%) aligned >1 times 76.61% overall alignment rate Time searching: 00:03:25 Overall time: 00:03:25 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 8 files... [bam_rmdupse_core] 1626721 / 11157195 = 0.1458 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 12:59:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.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, 11 Dec 2021 12:59:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:59:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:59:53: 1000000 INFO @ Sat, 11 Dec 2021 13:00:01: 2000000 INFO @ Sat, 11 Dec 2021 13:00:10: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 13:00:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.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, 11 Dec 2021 13:00:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:00:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:00:18: 4000000 INFO @ Sat, 11 Dec 2021 13:00:24: 1000000 INFO @ Sat, 11 Dec 2021 13:00:26: 5000000 INFO @ Sat, 11 Dec 2021 13:00:33: 2000000 INFO @ Sat, 11 Dec 2021 13:00:34: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 13:00:42: 3000000 INFO @ Sat, 11 Dec 2021 13:00:43: 7000000 INFO @ Sat, 11 Dec 2021 13:00:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.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, 11 Dec 2021 13:00:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:00:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:00:52: 8000000 INFO @ Sat, 11 Dec 2021 13:00:52: 4000000 INFO @ Sat, 11 Dec 2021 13:00:53: 1000000 INFO @ Sat, 11 Dec 2021 13:01:01: 9000000 INFO @ Sat, 11 Dec 2021 13:01:02: 2000000 INFO @ Sat, 11 Dec 2021 13:01:02: 5000000 INFO @ Sat, 11 Dec 2021 13:01:06: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:01:06: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:01:06: #1 total tags in treatment: 9530474 INFO @ Sat, 11 Dec 2021 13:01:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:01:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:01:06: #1 tags after filtering in treatment: 9530370 INFO @ Sat, 11 Dec 2021 13:01:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:01:06: #1 finished! INFO @ Sat, 11 Dec 2021 13:01:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:01:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:01:07: #2 number of paired peaks: 196 WARNING @ Sat, 11 Dec 2021 13:01:07: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Sat, 11 Dec 2021 13:01:07: start model_add_line... INFO @ Sat, 11 Dec 2021 13:01:07: start X-correlation... INFO @ Sat, 11 Dec 2021 13:01:07: end of X-cor INFO @ Sat, 11 Dec 2021 13:01:07: #2 finished! INFO @ Sat, 11 Dec 2021 13:01:07: #2 predicted fragment length is 86 bps INFO @ Sat, 11 Dec 2021 13:01:07: #2 alternative fragment length(s) may be 3,27,63,86 bps INFO @ Sat, 11 Dec 2021 13:01:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.05_model.r WARNING @ Sat, 11 Dec 2021 13:01:07: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:01:07: #2 You may need to consider one of the other alternative d(s): 3,27,63,86 WARNING @ Sat, 11 Dec 2021 13:01:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 13:01:07: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:01:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:01:10: 3000000 INFO @ Sat, 11 Dec 2021 13:01:13: 6000000 INFO @ Sat, 11 Dec 2021 13:01:18: 4000000 INFO @ Sat, 11 Dec 2021 13:01:23: 7000000 INFO @ Sat, 11 Dec 2021 13:01:26: 5000000 INFO @ Sat, 11 Dec 2021 13:01:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:01:34: 6000000 INFO @ Sat, 11 Dec 2021 13:01:34: 8000000 INFO @ Sat, 11 Dec 2021 13:01:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:01:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:01:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.05_summits.bed INFO @ Sat, 11 Dec 2021 13:01:37: Done! pass1 - making usageList (298 chroms): 1 millis pass2 - checking and writing primary data (736 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:01:42: 7000000 INFO @ Sat, 11 Dec 2021 13:01:44: 9000000 INFO @ Sat, 11 Dec 2021 13:01:50: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:01:50: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:01:50: #1 total tags in treatment: 9530474 INFO @ Sat, 11 Dec 2021 13:01:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:01:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:01:50: #1 tags after filtering in treatment: 9530370 INFO @ Sat, 11 Dec 2021 13:01:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:01:50: #1 finished! INFO @ Sat, 11 Dec 2021 13:01:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:01:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:01:51: 8000000 INFO @ Sat, 11 Dec 2021 13:01:51: #2 number of paired peaks: 196 WARNING @ Sat, 11 Dec 2021 13:01:51: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Sat, 11 Dec 2021 13:01:51: start model_add_line... INFO @ Sat, 11 Dec 2021 13:01:51: start X-correlation... INFO @ Sat, 11 Dec 2021 13:01:51: end of X-cor INFO @ Sat, 11 Dec 2021 13:01:51: #2 finished! INFO @ Sat, 11 Dec 2021 13:01:51: #2 predicted fragment length is 86 bps INFO @ Sat, 11 Dec 2021 13:01:51: #2 alternative fragment length(s) may be 3,27,63,86 bps INFO @ Sat, 11 Dec 2021 13:01:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.10_model.r WARNING @ Sat, 11 Dec 2021 13:01:51: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:01:51: #2 You may need to consider one of the other alternative d(s): 3,27,63,86 WARNING @ Sat, 11 Dec 2021 13:01:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 13:01:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:01:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:01:59: 9000000 INFO @ Sat, 11 Dec 2021 13:02:03: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:02:03: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:02:03: #1 total tags in treatment: 9530474 INFO @ Sat, 11 Dec 2021 13:02:03: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:02:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:02:04: #1 tags after filtering in treatment: 9530370 INFO @ Sat, 11 Dec 2021 13:02:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:02:04: #1 finished! INFO @ Sat, 11 Dec 2021 13:02:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:02:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:02:05: #2 number of paired peaks: 196 WARNING @ Sat, 11 Dec 2021 13:02:05: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Sat, 11 Dec 2021 13:02:05: start model_add_line... INFO @ Sat, 11 Dec 2021 13:02:05: start X-correlation... INFO @ Sat, 11 Dec 2021 13:02:05: end of X-cor INFO @ Sat, 11 Dec 2021 13:02:05: #2 finished! INFO @ Sat, 11 Dec 2021 13:02:05: #2 predicted fragment length is 86 bps INFO @ Sat, 11 Dec 2021 13:02:05: #2 alternative fragment length(s) may be 3,27,63,86 bps INFO @ Sat, 11 Dec 2021 13:02:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.20_model.r WARNING @ Sat, 11 Dec 2021 13:02:05: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:02:05: #2 You may need to consider one of the other alternative d(s): 3,27,63,86 WARNING @ Sat, 11 Dec 2021 13:02:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 13:02:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:02:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:02:10: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:02:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:02:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:02:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.10_summits.bed INFO @ Sat, 11 Dec 2021 13:02:21: Done! pass1 - making usageList (122 chroms): 1 millis pass2 - checking and writing primary data (252 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:02:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:02:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:02:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:02:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986153/SRX9986153.20_summits.bed INFO @ Sat, 11 Dec 2021 13:02:34: Done! pass1 - making usageList (56 chroms): 1 millis pass2 - checking and writing primary data (94 records, 4 fields): 5 millis CompletedMACS2peakCalling