Job ID = 14168546 SRX = SRX8688966 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: 00:02:23 7713106 reads; of these: 7713106 (100.00%) were unpaired; of these: 228589 (2.96%) aligned 0 times 5410569 (70.15%) aligned exactly 1 time 2073948 (26.89%) aligned >1 times 97.04% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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] 647641 / 7484517 = 0.0865 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 19:08:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.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 19:08:53: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:08:53: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:09:00: 1000000 INFO @ Fri, 10 Dec 2021 19:09:07: 2000000 INFO @ Fri, 10 Dec 2021 19:09:13: 3000000 INFO @ Fri, 10 Dec 2021 19:09:20: 4000000 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 19:09:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.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 19:09:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:09:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:09:26: 5000000 INFO @ Fri, 10 Dec 2021 19:09:31: 1000000 INFO @ Fri, 10 Dec 2021 19:09:34: 6000000 INFO @ Fri, 10 Dec 2021 19:09:38: 2000000 INFO @ Fri, 10 Dec 2021 19:09:40: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 19:09:40: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 19:09:40: #1 total tags in treatment: 6836876 INFO @ Fri, 10 Dec 2021 19:09:40: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:09:40: #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 19:09:40: #1 tags after filtering in treatment: 6836699 INFO @ Fri, 10 Dec 2021 19:09:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 19:09:40: #1 finished! INFO @ Fri, 10 Dec 2021 19:09:40: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:09:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:09:41: #2 number of paired peaks: 853 WARNING @ Fri, 10 Dec 2021 19:09:41: Fewer paired peaks (853) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 853 pairs to build model! INFO @ Fri, 10 Dec 2021 19:09:41: start model_add_line... INFO @ Fri, 10 Dec 2021 19:09:41: start X-correlation... INFO @ Fri, 10 Dec 2021 19:09:41: end of X-cor INFO @ Fri, 10 Dec 2021 19:09:41: #2 finished! INFO @ Fri, 10 Dec 2021 19:09:41: #2 predicted fragment length is 61 bps INFO @ Fri, 10 Dec 2021 19:09:41: #2 alternative fragment length(s) may be 61 bps INFO @ Fri, 10 Dec 2021 19:09:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.05_model.r WARNING @ Fri, 10 Dec 2021 19:09:41: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:09:41: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Fri, 10 Dec 2021 19:09:41: #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 19:09:41: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:09:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:09:44: 3000000 INFO @ Fri, 10 Dec 2021 19:09:51: 4000000 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 19:09:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.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 19:09:53: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:09:53: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:09:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:09:57: 5000000 INFO @ Fri, 10 Dec 2021 19:10:01: 1000000 INFO @ Fri, 10 Dec 2021 19:10:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:10:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:10:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.05_summits.bed INFO @ Fri, 10 Dec 2021 19:10:01: Done! pass1 - making usageList (582 chroms): 1 millis pass2 - checking and writing primary data (2157 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:10:04: 6000000 INFO @ Fri, 10 Dec 2021 19:10:08: 2000000 INFO @ Fri, 10 Dec 2021 19:10:10: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 19:10:10: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 19:10:10: #1 total tags in treatment: 6836876 INFO @ Fri, 10 Dec 2021 19:10:10: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:10:10: #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 19:10:10: #1 tags after filtering in treatment: 6836699 INFO @ Fri, 10 Dec 2021 19:10:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 19:10:10: #1 finished! INFO @ Fri, 10 Dec 2021 19:10:10: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:10:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:10:11: #2 number of paired peaks: 853 WARNING @ Fri, 10 Dec 2021 19:10:11: Fewer paired peaks (853) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 853 pairs to build model! INFO @ Fri, 10 Dec 2021 19:10:11: start model_add_line... INFO @ Fri, 10 Dec 2021 19:10:11: start X-correlation... INFO @ Fri, 10 Dec 2021 19:10:11: end of X-cor INFO @ Fri, 10 Dec 2021 19:10:11: #2 finished! INFO @ Fri, 10 Dec 2021 19:10:11: #2 predicted fragment length is 61 bps INFO @ Fri, 10 Dec 2021 19:10:11: #2 alternative fragment length(s) may be 61 bps INFO @ Fri, 10 Dec 2021 19:10:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.10_model.r WARNING @ Fri, 10 Dec 2021 19:10:11: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:10:11: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Fri, 10 Dec 2021 19:10:11: #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 19:10:11: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:10:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:10:15: 3000000 INFO @ Fri, 10 Dec 2021 19:10:22: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:10:25: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:10:29: 5000000 INFO @ Fri, 10 Dec 2021 19:10:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:10:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:10:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.10_summits.bed INFO @ Fri, 10 Dec 2021 19:10:32: Done! pass1 - making usageList (421 chroms): 1 millis pass2 - checking and writing primary data (1111 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:10:36: 6000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:10:42: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 19:10:42: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 19:10:42: #1 total tags in treatment: 6836876 INFO @ Fri, 10 Dec 2021 19:10:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:10:42: #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 19:10:43: #1 tags after filtering in treatment: 6836699 INFO @ Fri, 10 Dec 2021 19:10:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 19:10:43: #1 finished! INFO @ Fri, 10 Dec 2021 19:10:43: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:10:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:10:43: #2 number of paired peaks: 853 WARNING @ Fri, 10 Dec 2021 19:10:43: Fewer paired peaks (853) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 853 pairs to build model! INFO @ Fri, 10 Dec 2021 19:10:43: start model_add_line... INFO @ Fri, 10 Dec 2021 19:10:43: start X-correlation... INFO @ Fri, 10 Dec 2021 19:10:43: end of X-cor INFO @ Fri, 10 Dec 2021 19:10:43: #2 finished! INFO @ Fri, 10 Dec 2021 19:10:43: #2 predicted fragment length is 61 bps INFO @ Fri, 10 Dec 2021 19:10:43: #2 alternative fragment length(s) may be 61 bps INFO @ Fri, 10 Dec 2021 19:10:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.20_model.r WARNING @ Fri, 10 Dec 2021 19:10:43: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:10:43: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Fri, 10 Dec 2021 19:10:43: #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 19:10:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:10:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:10:57: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:11:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:11:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:11:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688966/SRX8688966.20_summits.bed INFO @ Fri, 10 Dec 2021 19:11:04: Done! pass1 - making usageList (185 chroms): 0 millis pass2 - checking and writing primary data (347 records, 4 fields): 7 millis CompletedMACS2peakCalling