Job ID = 14168072 SRX = SRX8688941 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: 00:05:47 21177474 reads; of these: 21177474 (100.00%) were unpaired; of these: 607260 (2.87%) aligned 0 times 14838589 (70.07%) aligned exactly 1 time 5731625 (27.06%) aligned >1 times 97.13% overall alignment rate Time searching: 00:05:47 Overall time: 00:05:47 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] 2724629 / 20570214 = 0.1325 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 @ Fri, 10 Dec 2021 15:12:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.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 @ Fri, 10 Dec 2021 15:12:45: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:12:45: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:12:52: 1000000 INFO @ Fri, 10 Dec 2021 15:12:59: 2000000 INFO @ Fri, 10 Dec 2021 15:13:07: 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 @ Fri, 10 Dec 2021 15:13:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.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 @ Fri, 10 Dec 2021 15:13:14: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:13:14: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:13:14: 4000000 INFO @ Fri, 10 Dec 2021 15:13:23: 1000000 INFO @ Fri, 10 Dec 2021 15:13:23: 5000000 INFO @ Fri, 10 Dec 2021 15:13:31: 2000000 INFO @ Fri, 10 Dec 2021 15:13:31: 6000000 INFO @ Fri, 10 Dec 2021 15:13:39: 3000000 INFO @ Fri, 10 Dec 2021 15:13:40: 7000000 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 @ Fri, 10 Dec 2021 15:13:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.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 @ Fri, 10 Dec 2021 15:13:44: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:13:44: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:13:47: 4000000 INFO @ Fri, 10 Dec 2021 15:13:48: 8000000 INFO @ Fri, 10 Dec 2021 15:13:52: 1000000 INFO @ Fri, 10 Dec 2021 15:13:56: 5000000 INFO @ Fri, 10 Dec 2021 15:13:57: 9000000 INFO @ Fri, 10 Dec 2021 15:14:00: 2000000 INFO @ Fri, 10 Dec 2021 15:14:04: 6000000 INFO @ Fri, 10 Dec 2021 15:14:05: 10000000 INFO @ Fri, 10 Dec 2021 15:14:08: 3000000 INFO @ Fri, 10 Dec 2021 15:14:13: 7000000 INFO @ Fri, 10 Dec 2021 15:14:14: 11000000 INFO @ Fri, 10 Dec 2021 15:14:15: 4000000 INFO @ Fri, 10 Dec 2021 15:14:21: 8000000 INFO @ Fri, 10 Dec 2021 15:14:22: 12000000 INFO @ Fri, 10 Dec 2021 15:14:23: 5000000 INFO @ Fri, 10 Dec 2021 15:14:29: 9000000 INFO @ Fri, 10 Dec 2021 15:14:31: 6000000 INFO @ Fri, 10 Dec 2021 15:14:31: 13000000 INFO @ Fri, 10 Dec 2021 15:14:38: 10000000 INFO @ Fri, 10 Dec 2021 15:14:38: 7000000 INFO @ Fri, 10 Dec 2021 15:14:40: 14000000 INFO @ Fri, 10 Dec 2021 15:14:46: 8000000 INFO @ Fri, 10 Dec 2021 15:14:46: 11000000 INFO @ Fri, 10 Dec 2021 15:14:48: 15000000 INFO @ Fri, 10 Dec 2021 15:14:54: 9000000 INFO @ Fri, 10 Dec 2021 15:14:54: 12000000 INFO @ Fri, 10 Dec 2021 15:14:57: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 15:15:01: 10000000 INFO @ Fri, 10 Dec 2021 15:15:03: 13000000 INFO @ Fri, 10 Dec 2021 15:15:05: 17000000 INFO @ Fri, 10 Dec 2021 15:15:09: 11000000 INFO @ Fri, 10 Dec 2021 15:15:11: 14000000 INFO @ Fri, 10 Dec 2021 15:15:13: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:15:13: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:15:13: #1 total tags in treatment: 17845585 INFO @ Fri, 10 Dec 2021 15:15:13: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:15:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 15:15:13: #1 tags after filtering in treatment: 17845536 INFO @ Fri, 10 Dec 2021 15:15:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:15:13: #1 finished! INFO @ Fri, 10 Dec 2021 15:15:13: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:15:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:15:14: #2 number of paired peaks: 672 WARNING @ Fri, 10 Dec 2021 15:15:14: Fewer paired peaks (672) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 672 pairs to build model! INFO @ Fri, 10 Dec 2021 15:15:14: start model_add_line... INFO @ Fri, 10 Dec 2021 15:15:14: start X-correlation... INFO @ Fri, 10 Dec 2021 15:15:14: end of X-cor INFO @ Fri, 10 Dec 2021 15:15:14: #2 finished! INFO @ Fri, 10 Dec 2021 15:15:14: #2 predicted fragment length is 53 bps INFO @ Fri, 10 Dec 2021 15:15:14: #2 alternative fragment length(s) may be 4,53 bps INFO @ Fri, 10 Dec 2021 15:15:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.05_model.r WARNING @ Fri, 10 Dec 2021 15:15:15: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:15:15: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Fri, 10 Dec 2021 15:15:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 15:15:15: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:15:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:15:16: 12000000 INFO @ Fri, 10 Dec 2021 15:15:20: 15000000 INFO @ Fri, 10 Dec 2021 15:15:24: 13000000 INFO @ Fri, 10 Dec 2021 15:15:28: 16000000 INFO @ Fri, 10 Dec 2021 15:15:32: 14000000 INFO @ Fri, 10 Dec 2021 15:15:36: 17000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 15:15:39: 15000000 INFO @ Fri, 10 Dec 2021 15:15:43: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:15:43: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:15:43: #1 total tags in treatment: 17845585 INFO @ Fri, 10 Dec 2021 15:15:43: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:15:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 15:15:44: #1 tags after filtering in treatment: 17845536 INFO @ Fri, 10 Dec 2021 15:15:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:15:44: #1 finished! INFO @ Fri, 10 Dec 2021 15:15:44: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:15:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:15:45: #2 number of paired peaks: 672 WARNING @ Fri, 10 Dec 2021 15:15:45: Fewer paired peaks (672) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 672 pairs to build model! INFO @ Fri, 10 Dec 2021 15:15:45: start model_add_line... INFO @ Fri, 10 Dec 2021 15:15:45: start X-correlation... INFO @ Fri, 10 Dec 2021 15:15:45: end of X-cor INFO @ Fri, 10 Dec 2021 15:15:45: #2 finished! INFO @ Fri, 10 Dec 2021 15:15:45: #2 predicted fragment length is 53 bps INFO @ Fri, 10 Dec 2021 15:15:45: #2 alternative fragment length(s) may be 4,53 bps INFO @ Fri, 10 Dec 2021 15:15:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.10_model.r WARNING @ Fri, 10 Dec 2021 15:15:45: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:15:45: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Fri, 10 Dec 2021 15:15:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 15:15:45: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:15:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:15:46: 16000000 INFO @ Fri, 10 Dec 2021 15:15:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:15:53: 17000000 INFO @ Fri, 10 Dec 2021 15:15:58: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:15:58: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:15:58: #1 total tags in treatment: 17845585 INFO @ Fri, 10 Dec 2021 15:15:58: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:15:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 15:15:58: #1 tags after filtering in treatment: 17845536 INFO @ Fri, 10 Dec 2021 15:15:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:15:58: #1 finished! INFO @ Fri, 10 Dec 2021 15:15:58: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:15:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:16:00: #2 number of paired peaks: 672 WARNING @ Fri, 10 Dec 2021 15:16:00: Fewer paired peaks (672) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 672 pairs to build model! INFO @ Fri, 10 Dec 2021 15:16:00: start model_add_line... INFO @ Fri, 10 Dec 2021 15:16:00: start X-correlation... INFO @ Fri, 10 Dec 2021 15:16:00: end of X-cor INFO @ Fri, 10 Dec 2021 15:16:00: #2 finished! INFO @ Fri, 10 Dec 2021 15:16:00: #2 predicted fragment length is 53 bps INFO @ Fri, 10 Dec 2021 15:16:00: #2 alternative fragment length(s) may be 4,53 bps INFO @ Fri, 10 Dec 2021 15:16:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.20_model.r WARNING @ Fri, 10 Dec 2021 15:16:00: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:16:00: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Fri, 10 Dec 2021 15:16:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 15:16:00: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:16:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:16:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.05_peaks.xls INFO @ Fri, 10 Dec 2021 15:16:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:16:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.05_summits.bed INFO @ Fri, 10 Dec 2021 15:16:03: Done! pass1 - making usageList (714 chroms): 1 millis pass2 - checking and writing primary data (3600 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:16:18: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:16:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:16:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.10_peaks.xls INFO @ Fri, 10 Dec 2021 15:16:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:16:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.10_summits.bed INFO @ Fri, 10 Dec 2021 15:16:33: Done! pass1 - making usageList (611 chroms): 1 millis pass2 - checking and writing primary data (2264 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:16:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.20_peaks.xls INFO @ Fri, 10 Dec 2021 15:16:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:16:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688941/SRX8688941.20_summits.bed INFO @ Fri, 10 Dec 2021 15:16:48: Done! pass1 - making usageList (336 chroms): 1 millis pass2 - checking and writing primary data (831 records, 4 fields): 10 millis CompletedMACS2peakCalling