Job ID = 14169097 SRX = SRX8688992 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: 00:06:20 20004097 reads; of these: 20004097 (100.00%) were unpaired; of these: 1000990 (5.00%) aligned 0 times 15074710 (75.36%) aligned exactly 1 time 3928397 (19.64%) aligned >1 times 95.00% overall alignment rate Time searching: 00:06:20 Overall time: 00:06:20 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] 2091586 / 19003107 = 0.1101 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 23:53:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.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 23:53:21: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:53:21: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:53:31: 1000000 INFO @ Fri, 10 Dec 2021 23:53:41: 2000000 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 23:53:50: 3000000 INFO @ Fri, 10 Dec 2021 23:53:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.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 23:53:51: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:53:51: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:54:00: 4000000 INFO @ Fri, 10 Dec 2021 23:54:01: 1000000 INFO @ Fri, 10 Dec 2021 23:54:10: 5000000 INFO @ Fri, 10 Dec 2021 23:54:12: 2000000 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 23:54:20: 6000000 INFO @ Fri, 10 Dec 2021 23:54:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.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 23:54:21: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:54:21: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:54:22: 3000000 INFO @ Fri, 10 Dec 2021 23:54:30: 7000000 INFO @ Fri, 10 Dec 2021 23:54:32: 4000000 INFO @ Fri, 10 Dec 2021 23:54:33: 1000000 INFO @ Fri, 10 Dec 2021 23:54:40: 8000000 INFO @ Fri, 10 Dec 2021 23:54:42: 5000000 INFO @ Fri, 10 Dec 2021 23:54:45: 2000000 INFO @ Fri, 10 Dec 2021 23:54:50: 9000000 INFO @ Fri, 10 Dec 2021 23:54:53: 6000000 INFO @ Fri, 10 Dec 2021 23:54:57: 3000000 INFO @ Fri, 10 Dec 2021 23:55:00: 10000000 INFO @ Fri, 10 Dec 2021 23:55:03: 7000000 INFO @ Fri, 10 Dec 2021 23:55:08: 4000000 INFO @ Fri, 10 Dec 2021 23:55:10: 11000000 INFO @ Fri, 10 Dec 2021 23:55:14: 8000000 INFO @ Fri, 10 Dec 2021 23:55:20: 5000000 INFO @ Fri, 10 Dec 2021 23:55:21: 12000000 INFO @ Fri, 10 Dec 2021 23:55:24: 9000000 INFO @ Fri, 10 Dec 2021 23:55:31: 13000000 INFO @ Fri, 10 Dec 2021 23:55:32: 6000000 INFO @ Fri, 10 Dec 2021 23:55:35: 10000000 INFO @ Fri, 10 Dec 2021 23:55:42: 14000000 INFO @ Fri, 10 Dec 2021 23:55:44: 7000000 INFO @ Fri, 10 Dec 2021 23:55:45: 11000000 INFO @ Fri, 10 Dec 2021 23:55:52: 15000000 INFO @ Fri, 10 Dec 2021 23:55:55: 12000000 INFO @ Fri, 10 Dec 2021 23:55:56: 8000000 INFO @ Fri, 10 Dec 2021 23:56:02: 16000000 INFO @ Fri, 10 Dec 2021 23:56:05: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 23:56:08: 9000000 INFO @ Fri, 10 Dec 2021 23:56:12: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 23:56:12: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 23:56:12: #1 total tags in treatment: 16911521 INFO @ Fri, 10 Dec 2021 23:56:12: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:56:12: #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 23:56:12: #1 tags after filtering in treatment: 16911417 INFO @ Fri, 10 Dec 2021 23:56:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 23:56:12: #1 finished! INFO @ Fri, 10 Dec 2021 23:56:12: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:56:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:56:14: #2 number of paired peaks: 496 WARNING @ Fri, 10 Dec 2021 23:56:14: Fewer paired peaks (496) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 496 pairs to build model! INFO @ Fri, 10 Dec 2021 23:56:14: start model_add_line... INFO @ Fri, 10 Dec 2021 23:56:14: start X-correlation... INFO @ Fri, 10 Dec 2021 23:56:14: end of X-cor INFO @ Fri, 10 Dec 2021 23:56:14: #2 finished! INFO @ Fri, 10 Dec 2021 23:56:14: #2 predicted fragment length is 57 bps INFO @ Fri, 10 Dec 2021 23:56:14: #2 alternative fragment length(s) may be 4,57 bps INFO @ Fri, 10 Dec 2021 23:56:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.05_model.r WARNING @ Fri, 10 Dec 2021 23:56:14: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 23:56:14: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Fri, 10 Dec 2021 23:56:14: #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 23:56:14: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:56:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 23:56:16: 14000000 INFO @ Fri, 10 Dec 2021 23:56:20: 10000000 INFO @ Fri, 10 Dec 2021 23:56:26: 15000000 INFO @ Fri, 10 Dec 2021 23:56:31: 11000000 INFO @ Fri, 10 Dec 2021 23:56:37: 16000000 INFO @ Fri, 10 Dec 2021 23:56:43: 12000000 INFO @ Fri, 10 Dec 2021 23:56:46: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 23:56:46: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 23:56:46: #1 total tags in treatment: 16911521 INFO @ Fri, 10 Dec 2021 23:56:46: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:56:46: #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 23:56:47: #1 tags after filtering in treatment: 16911417 INFO @ Fri, 10 Dec 2021 23:56:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 23:56:47: #1 finished! INFO @ Fri, 10 Dec 2021 23:56:47: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:56:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:56:49: #2 number of paired peaks: 496 WARNING @ Fri, 10 Dec 2021 23:56:49: Fewer paired peaks (496) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 496 pairs to build model! INFO @ Fri, 10 Dec 2021 23:56:49: start model_add_line... INFO @ Fri, 10 Dec 2021 23:56:49: start X-correlation... INFO @ Fri, 10 Dec 2021 23:56:49: end of X-cor INFO @ Fri, 10 Dec 2021 23:56:49: #2 finished! INFO @ Fri, 10 Dec 2021 23:56:49: #2 predicted fragment length is 57 bps INFO @ Fri, 10 Dec 2021 23:56:49: #2 alternative fragment length(s) may be 4,57 bps INFO @ Fri, 10 Dec 2021 23:56:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.10_model.r WARNING @ Fri, 10 Dec 2021 23:56:49: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 23:56:49: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Fri, 10 Dec 2021 23:56:49: #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 23:56:49: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:56:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 23:56:55: 13000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 23:56:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:57:07: 14000000 INFO @ Fri, 10 Dec 2021 23:57:18: 15000000 INFO @ Fri, 10 Dec 2021 23:57:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.05_peaks.xls INFO @ Fri, 10 Dec 2021 23:57:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:57:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.05_summits.bed INFO @ Fri, 10 Dec 2021 23:57:20: Done! pass1 - making usageList (461 chroms): 2 millis pass2 - checking and writing primary data (2550 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 23:57:30: 16000000 INFO @ Fri, 10 Dec 2021 23:57:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:57:40: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 23:57:40: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 23:57:40: #1 total tags in treatment: 16911521 INFO @ Fri, 10 Dec 2021 23:57:40: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:57:40: #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 23:57:41: #1 tags after filtering in treatment: 16911417 INFO @ Fri, 10 Dec 2021 23:57:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 23:57:41: #1 finished! INFO @ Fri, 10 Dec 2021 23:57:41: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:57:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:57:43: #2 number of paired peaks: 496 WARNING @ Fri, 10 Dec 2021 23:57:43: Fewer paired peaks (496) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 496 pairs to build model! INFO @ Fri, 10 Dec 2021 23:57:43: start model_add_line... INFO @ Fri, 10 Dec 2021 23:57:43: start X-correlation... INFO @ Fri, 10 Dec 2021 23:57:43: end of X-cor INFO @ Fri, 10 Dec 2021 23:57:43: #2 finished! INFO @ Fri, 10 Dec 2021 23:57:43: #2 predicted fragment length is 57 bps INFO @ Fri, 10 Dec 2021 23:57:43: #2 alternative fragment length(s) may be 4,57 bps INFO @ Fri, 10 Dec 2021 23:57:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.20_model.r WARNING @ Fri, 10 Dec 2021 23:57:43: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 23:57:43: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Fri, 10 Dec 2021 23:57:43: #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 23:57:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:57:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 23:57:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.10_peaks.xls INFO @ Fri, 10 Dec 2021 23:57:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:57:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.10_summits.bed INFO @ Fri, 10 Dec 2021 23:57:56: Done! pass1 - making usageList (302 chroms): 2 millis pass2 - checking and writing primary data (1116 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 23:58:28: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:58:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.20_peaks.xls INFO @ Fri, 10 Dec 2021 23:58:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:58:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688992/SRX8688992.20_summits.bed INFO @ Fri, 10 Dec 2021 23:58:49: Done! pass1 - making usageList (205 chroms): 1 millis pass2 - checking and writing primary data (564 records, 4 fields): 12 millis CompletedMACS2peakCalling