Job ID = 6529419 SRX = SRX2618493 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: 00:06:19 23114100 reads; of these: 23114100 (100.00%) were unpaired; of these: 1180755 (5.11%) aligned 0 times 18075014 (78.20%) aligned exactly 1 time 3858331 (16.69%) aligned >1 times 94.89% overall alignment rate Time searching: 00:06:19 Overall time: 00:06:19 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] 2533616 / 21933345 = 0.1155 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:04:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.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, 30 Jun 2020 02:04:12: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:04:12: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:04:17: 1000000 INFO @ Tue, 30 Jun 2020 02:04:23: 2000000 INFO @ Tue, 30 Jun 2020 02:04:29: 3000000 INFO @ Tue, 30 Jun 2020 02:04:34: 4000000 INFO @ Tue, 30 Jun 2020 02:04:40: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:04:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.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, 30 Jun 2020 02:04:42: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:04:42: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:04:45: 6000000 INFO @ Tue, 30 Jun 2020 02:04:47: 1000000 INFO @ Tue, 30 Jun 2020 02:04:51: 7000000 INFO @ Tue, 30 Jun 2020 02:04:53: 2000000 INFO @ Tue, 30 Jun 2020 02:04:57: 8000000 INFO @ Tue, 30 Jun 2020 02:04:58: 3000000 INFO @ Tue, 30 Jun 2020 02:05:03: 9000000 INFO @ Tue, 30 Jun 2020 02:05:03: 4000000 INFO @ Tue, 30 Jun 2020 02:05:08: 10000000 INFO @ Tue, 30 Jun 2020 02:05:09: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:05:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.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, 30 Jun 2020 02:05:12: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:05:12: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:05:14: 6000000 INFO @ Tue, 30 Jun 2020 02:05:14: 11000000 INFO @ Tue, 30 Jun 2020 02:05:18: 1000000 INFO @ Tue, 30 Jun 2020 02:05:19: 7000000 INFO @ Tue, 30 Jun 2020 02:05:20: 12000000 INFO @ Tue, 30 Jun 2020 02:05:24: 2000000 INFO @ Tue, 30 Jun 2020 02:05:24: 8000000 INFO @ Tue, 30 Jun 2020 02:05:25: 13000000 INFO @ Tue, 30 Jun 2020 02:05:29: 9000000 INFO @ Tue, 30 Jun 2020 02:05:29: 3000000 INFO @ Tue, 30 Jun 2020 02:05:31: 14000000 INFO @ Tue, 30 Jun 2020 02:05:34: 10000000 INFO @ Tue, 30 Jun 2020 02:05:35: 4000000 INFO @ Tue, 30 Jun 2020 02:05:36: 15000000 INFO @ Tue, 30 Jun 2020 02:05:40: 11000000 INFO @ Tue, 30 Jun 2020 02:05:41: 5000000 INFO @ Tue, 30 Jun 2020 02:05:42: 16000000 INFO @ Tue, 30 Jun 2020 02:05:45: 12000000 INFO @ Tue, 30 Jun 2020 02:05:47: 6000000 INFO @ Tue, 30 Jun 2020 02:05:48: 17000000 INFO @ Tue, 30 Jun 2020 02:05:50: 13000000 INFO @ Tue, 30 Jun 2020 02:05:52: 7000000 INFO @ Tue, 30 Jun 2020 02:05:53: 18000000 INFO @ Tue, 30 Jun 2020 02:05:55: 14000000 INFO @ Tue, 30 Jun 2020 02:05:58: 8000000 INFO @ Tue, 30 Jun 2020 02:05:59: 19000000 INFO @ Tue, 30 Jun 2020 02:06:01: 15000000 INFO @ Tue, 30 Jun 2020 02:06:01: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:06:01: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:06:01: #1 total tags in treatment: 19399729 INFO @ Tue, 30 Jun 2020 02:06:01: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:06:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:06:02: #1 tags after filtering in treatment: 19399724 INFO @ Tue, 30 Jun 2020 02:06:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:06:02: #1 finished! INFO @ Tue, 30 Jun 2020 02:06:02: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:06:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:06:03: #2 number of paired peaks: 344 WARNING @ Tue, 30 Jun 2020 02:06:03: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Tue, 30 Jun 2020 02:06:03: start model_add_line... INFO @ Tue, 30 Jun 2020 02:06:03: start X-correlation... INFO @ Tue, 30 Jun 2020 02:06:03: end of X-cor INFO @ Tue, 30 Jun 2020 02:06:03: #2 finished! INFO @ Tue, 30 Jun 2020 02:06:03: #2 predicted fragment length is 40 bps INFO @ Tue, 30 Jun 2020 02:06:03: #2 alternative fragment length(s) may be 2,40,522,575 bps INFO @ Tue, 30 Jun 2020 02:06:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.05_model.r WARNING @ Tue, 30 Jun 2020 02:06:03: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:06:03: #2 You may need to consider one of the other alternative d(s): 2,40,522,575 WARNING @ Tue, 30 Jun 2020 02:06:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:06:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:06:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:06:04: 9000000 INFO @ Tue, 30 Jun 2020 02:06:06: 16000000 INFO @ Tue, 30 Jun 2020 02:06:10: 10000000 INFO @ Tue, 30 Jun 2020 02:06:11: 17000000 INFO @ Tue, 30 Jun 2020 02:06:15: 11000000 INFO @ Tue, 30 Jun 2020 02:06:16: 18000000 INFO @ Tue, 30 Jun 2020 02:06:21: 12000000 INFO @ Tue, 30 Jun 2020 02:06:22: 19000000 INFO @ Tue, 30 Jun 2020 02:06:24: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:06:24: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:06:24: #1 total tags in treatment: 19399729 INFO @ Tue, 30 Jun 2020 02:06:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:06:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:06:24: #1 tags after filtering in treatment: 19399724 INFO @ Tue, 30 Jun 2020 02:06:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:06:24: #1 finished! INFO @ Tue, 30 Jun 2020 02:06:24: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:06:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:06:26: #2 number of paired peaks: 344 WARNING @ Tue, 30 Jun 2020 02:06:26: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Tue, 30 Jun 2020 02:06:26: start model_add_line... INFO @ Tue, 30 Jun 2020 02:06:26: start X-correlation... INFO @ Tue, 30 Jun 2020 02:06:26: end of X-cor INFO @ Tue, 30 Jun 2020 02:06:26: #2 finished! INFO @ Tue, 30 Jun 2020 02:06:26: #2 predicted fragment length is 40 bps INFO @ Tue, 30 Jun 2020 02:06:26: #2 alternative fragment length(s) may be 2,40,522,575 bps INFO @ Tue, 30 Jun 2020 02:06:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.10_model.r WARNING @ Tue, 30 Jun 2020 02:06:26: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:06:26: #2 You may need to consider one of the other alternative d(s): 2,40,522,575 WARNING @ Tue, 30 Jun 2020 02:06:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:06:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:06:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:06:27: 13000000 INFO @ Tue, 30 Jun 2020 02:06:32: 14000000 INFO @ Tue, 30 Jun 2020 02:06:38: 15000000 INFO @ Tue, 30 Jun 2020 02:06:39: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:06:44: 16000000 INFO @ Tue, 30 Jun 2020 02:06:49: 17000000 INFO @ Tue, 30 Jun 2020 02:06:55: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:06:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:06:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:06:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.05_summits.bed INFO @ Tue, 30 Jun 2020 02:06:57: Done! pass1 - making usageList (498 chroms): 1 millis pass2 - checking and writing primary data (1937 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:07:00: 19000000 INFO @ Tue, 30 Jun 2020 02:07:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:07:03: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:07:03: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:07:03: #1 total tags in treatment: 19399729 INFO @ Tue, 30 Jun 2020 02:07:03: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:07:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:07:03: #1 tags after filtering in treatment: 19399724 INFO @ Tue, 30 Jun 2020 02:07:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:07:03: #1 finished! INFO @ Tue, 30 Jun 2020 02:07:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:07:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:07:05: #2 number of paired peaks: 344 WARNING @ Tue, 30 Jun 2020 02:07:05: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Tue, 30 Jun 2020 02:07:05: start model_add_line... INFO @ Tue, 30 Jun 2020 02:07:05: start X-correlation... INFO @ Tue, 30 Jun 2020 02:07:05: end of X-cor INFO @ Tue, 30 Jun 2020 02:07:05: #2 finished! INFO @ Tue, 30 Jun 2020 02:07:05: #2 predicted fragment length is 40 bps INFO @ Tue, 30 Jun 2020 02:07:05: #2 alternative fragment length(s) may be 2,40,522,575 bps INFO @ Tue, 30 Jun 2020 02:07:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.20_model.r WARNING @ Tue, 30 Jun 2020 02:07:05: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:07:05: #2 You may need to consider one of the other alternative d(s): 2,40,522,575 WARNING @ Tue, 30 Jun 2020 02:07:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:07:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:07:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:07:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:07:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:07:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.10_summits.bed INFO @ Tue, 30 Jun 2020 02:07:18: Done! pass1 - making usageList (455 chroms): 1 millis pass2 - checking and writing primary data (1802 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:07:39: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:07:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:07:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:07:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618493/SRX2618493.20_summits.bed INFO @ Tue, 30 Jun 2020 02:07:55: Done! pass1 - making usageList (304 chroms): 1 millis pass2 - checking and writing primary data (677 records, 4 fields): 10 millis CompletedMACS2peakCalling