Job ID = 16439379 SRX = SRX15206498 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: 00:03:40 9931050 reads; of these: 9931050 (100.00%) were unpaired; of these: 307586 (3.10%) aligned 0 times 8447265 (85.06%) aligned exactly 1 time 1176199 (11.84%) aligned >1 times 96.90% overall alignment rate Time searching: 00:03:41 Overall time: 00:03:41 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_rmdupse_core] 530523 / 9623464 = 0.0551 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:08:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.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, 02 Aug 2022 15:08:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:08:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:08:59: 1000000 INFO @ Tue, 02 Aug 2022 15:09:07: 2000000 INFO @ Tue, 02 Aug 2022 15:09:14: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:09:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.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, 02 Aug 2022 15:09:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:09:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:09:22: 4000000 INFO @ Tue, 02 Aug 2022 15:09:29: 1000000 INFO @ Tue, 02 Aug 2022 15:09:30: 5000000 INFO @ Tue, 02 Aug 2022 15:09:37: 2000000 INFO @ Tue, 02 Aug 2022 15:09:38: 6000000 INFO @ Tue, 02 Aug 2022 15:09:44: 3000000 INFO @ Tue, 02 Aug 2022 15:09:45: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:09:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.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, 02 Aug 2022 15:09:50: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:09:50: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:09:52: 4000000 INFO @ Tue, 02 Aug 2022 15:09:54: 8000000 INFO @ Tue, 02 Aug 2022 15:09:59: 1000000 INFO @ Tue, 02 Aug 2022 15:10:00: 5000000 INFO @ Tue, 02 Aug 2022 15:10:02: 9000000 INFO @ Tue, 02 Aug 2022 15:10:03: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:10:03: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:10:03: #1 total tags in treatment: 9092941 INFO @ Tue, 02 Aug 2022 15:10:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:10:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:10:04: #1 tags after filtering in treatment: 9092743 INFO @ Tue, 02 Aug 2022 15:10:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:10:04: #1 finished! INFO @ Tue, 02 Aug 2022 15:10:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:10:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:10:04: #2 number of paired peaks: 256 WARNING @ Tue, 02 Aug 2022 15:10:04: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Tue, 02 Aug 2022 15:10:04: start model_add_line... INFO @ Tue, 02 Aug 2022 15:10:04: start X-correlation... INFO @ Tue, 02 Aug 2022 15:10:05: end of X-cor INFO @ Tue, 02 Aug 2022 15:10:05: #2 finished! INFO @ Tue, 02 Aug 2022 15:10:05: #2 predicted fragment length is 124 bps INFO @ Tue, 02 Aug 2022 15:10:05: #2 alternative fragment length(s) may be 124 bps INFO @ Tue, 02 Aug 2022 15:10:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.05_model.r WARNING @ Tue, 02 Aug 2022 15:10:05: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:10:05: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Tue, 02 Aug 2022 15:10:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:10:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:10:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:10:07: 2000000 INFO @ Tue, 02 Aug 2022 15:10:08: 6000000 INFO @ Tue, 02 Aug 2022 15:10:15: 3000000 INFO @ Tue, 02 Aug 2022 15:10:15: 7000000 INFO @ Tue, 02 Aug 2022 15:10:23: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:10:24: 4000000 INFO @ Tue, 02 Aug 2022 15:10:24: 8000000 INFO @ Tue, 02 Aug 2022 15:10:32: 9000000 INFO @ Tue, 02 Aug 2022 15:10:32: 5000000 INFO @ Tue, 02 Aug 2022 15:10:33: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:10:33: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:10:33: #1 total tags in treatment: 9092941 INFO @ Tue, 02 Aug 2022 15:10:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:10:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:10:33: #1 tags after filtering in treatment: 9092743 INFO @ Tue, 02 Aug 2022 15:10:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:10:33: #1 finished! INFO @ Tue, 02 Aug 2022 15:10:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:10:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:10:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:10:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:10:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.05_summits.bed INFO @ Tue, 02 Aug 2022 15:10:34: Done! pass1 - making usageList (96 chroms): 1 millis pass2 - checking and writing primary data (273 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:10:34: #2 number of paired peaks: 256 WARNING @ Tue, 02 Aug 2022 15:10:34: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Tue, 02 Aug 2022 15:10:34: start model_add_line... INFO @ Tue, 02 Aug 2022 15:10:34: start X-correlation... INFO @ Tue, 02 Aug 2022 15:10:34: end of X-cor INFO @ Tue, 02 Aug 2022 15:10:34: #2 finished! INFO @ Tue, 02 Aug 2022 15:10:34: #2 predicted fragment length is 124 bps INFO @ Tue, 02 Aug 2022 15:10:34: #2 alternative fragment length(s) may be 124 bps INFO @ Tue, 02 Aug 2022 15:10:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.10_model.r WARNING @ Tue, 02 Aug 2022 15:10:34: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:10:34: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Tue, 02 Aug 2022 15:10:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:10:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:10:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:10:40: 6000000 INFO @ Tue, 02 Aug 2022 15:10:48: 7000000 INFO @ Tue, 02 Aug 2022 15:10:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:10:57: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:11:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:11:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:11:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.10_summits.bed INFO @ Tue, 02 Aug 2022 15:11:03: Done! pass1 - making usageList (75 chroms): 2 millis pass2 - checking and writing primary data (162 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:11:05: 9000000 INFO @ Tue, 02 Aug 2022 15:11:06: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:11:06: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:11:06: #1 total tags in treatment: 9092941 INFO @ Tue, 02 Aug 2022 15:11:06: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:11:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:11:07: #1 tags after filtering in treatment: 9092743 INFO @ Tue, 02 Aug 2022 15:11:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:11:07: #1 finished! INFO @ Tue, 02 Aug 2022 15:11:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:11:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:11:08: #2 number of paired peaks: 256 WARNING @ Tue, 02 Aug 2022 15:11:08: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Tue, 02 Aug 2022 15:11:08: start model_add_line... INFO @ Tue, 02 Aug 2022 15:11:08: start X-correlation... INFO @ Tue, 02 Aug 2022 15:11:08: end of X-cor INFO @ Tue, 02 Aug 2022 15:11:08: #2 finished! INFO @ Tue, 02 Aug 2022 15:11:08: #2 predicted fragment length is 124 bps INFO @ Tue, 02 Aug 2022 15:11:08: #2 alternative fragment length(s) may be 124 bps INFO @ Tue, 02 Aug 2022 15:11:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.20_model.r WARNING @ Tue, 02 Aug 2022 15:11:08: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:11:08: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Tue, 02 Aug 2022 15:11:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:11:08: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:11:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:11:26: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:11:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:11:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:11:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206498/SRX15206498.20_summits.bed INFO @ Tue, 02 Aug 2022 15:11:36: Done! pass1 - making usageList (61 chroms): 1 millis pass2 - checking and writing primary data (114 records, 4 fields): 24 millis CompletedMACS2peakCalling