Job ID = 6529874 SRX = SRX5343136 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: 00:07:10 23202652 reads; of these: 23202652 (100.00%) were unpaired; of these: 1141394 (4.92%) aligned 0 times 19053282 (82.12%) aligned exactly 1 time 3007976 (12.96%) aligned >1 times 95.08% overall alignment rate Time searching: 00:07:10 Overall time: 00:07:10 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] 1928302 / 22061258 = 0.0874 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 03:00:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.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 03:00:04: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:00:04: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:00:10: 1000000 INFO @ Tue, 30 Jun 2020 03:00:17: 2000000 INFO @ Tue, 30 Jun 2020 03:00:24: 3000000 INFO @ Tue, 30 Jun 2020 03:00:30: 4000000 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 03:00:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.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 03:00:34: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:00:34: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:00:37: 5000000 INFO @ Tue, 30 Jun 2020 03:00:41: 1000000 INFO @ Tue, 30 Jun 2020 03:00:43: 6000000 INFO @ Tue, 30 Jun 2020 03:00:48: 2000000 INFO @ Tue, 30 Jun 2020 03:00:50: 7000000 INFO @ Tue, 30 Jun 2020 03:00:54: 3000000 INFO @ Tue, 30 Jun 2020 03:00:56: 8000000 INFO @ Tue, 30 Jun 2020 03:01:01: 4000000 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 03:01:03: 9000000 INFO @ Tue, 30 Jun 2020 03:01:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.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 03:01:04: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:01:04: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:01:08: 5000000 INFO @ Tue, 30 Jun 2020 03:01:10: 10000000 INFO @ Tue, 30 Jun 2020 03:01:10: 1000000 INFO @ Tue, 30 Jun 2020 03:01:14: 6000000 INFO @ Tue, 30 Jun 2020 03:01:16: 11000000 INFO @ Tue, 30 Jun 2020 03:01:17: 2000000 INFO @ Tue, 30 Jun 2020 03:01:21: 7000000 INFO @ Tue, 30 Jun 2020 03:01:23: 12000000 INFO @ Tue, 30 Jun 2020 03:01:24: 3000000 INFO @ Tue, 30 Jun 2020 03:01:27: 8000000 INFO @ Tue, 30 Jun 2020 03:01:29: 13000000 INFO @ Tue, 30 Jun 2020 03:01:30: 4000000 INFO @ Tue, 30 Jun 2020 03:01:34: 9000000 INFO @ Tue, 30 Jun 2020 03:01:36: 14000000 INFO @ Tue, 30 Jun 2020 03:01:37: 5000000 INFO @ Tue, 30 Jun 2020 03:01:41: 10000000 INFO @ Tue, 30 Jun 2020 03:01:42: 15000000 INFO @ Tue, 30 Jun 2020 03:01:43: 6000000 INFO @ Tue, 30 Jun 2020 03:01:47: 11000000 INFO @ Tue, 30 Jun 2020 03:01:49: 16000000 INFO @ Tue, 30 Jun 2020 03:01:50: 7000000 INFO @ Tue, 30 Jun 2020 03:01:54: 12000000 INFO @ Tue, 30 Jun 2020 03:01:55: 17000000 INFO @ Tue, 30 Jun 2020 03:01:56: 8000000 INFO @ Tue, 30 Jun 2020 03:02:00: 13000000 INFO @ Tue, 30 Jun 2020 03:02:02: 18000000 INFO @ Tue, 30 Jun 2020 03:02:03: 9000000 INFO @ Tue, 30 Jun 2020 03:02:07: 14000000 INFO @ Tue, 30 Jun 2020 03:02:09: 19000000 INFO @ Tue, 30 Jun 2020 03:02:09: 10000000 INFO @ Tue, 30 Jun 2020 03:02:14: 15000000 INFO @ Tue, 30 Jun 2020 03:02:15: 20000000 INFO @ Tue, 30 Jun 2020 03:02:15: 11000000 INFO @ Tue, 30 Jun 2020 03:02:16: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:02:16: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:02:16: #1 total tags in treatment: 20132956 INFO @ Tue, 30 Jun 2020 03:02:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:02:16: #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 03:02:17: #1 tags after filtering in treatment: 20132953 INFO @ Tue, 30 Jun 2020 03:02:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:02:17: #1 finished! INFO @ Tue, 30 Jun 2020 03:02:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:02:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:02:18: #2 number of paired peaks: 110 WARNING @ Tue, 30 Jun 2020 03:02:18: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Tue, 30 Jun 2020 03:02:18: start model_add_line... INFO @ Tue, 30 Jun 2020 03:02:19: start X-correlation... INFO @ Tue, 30 Jun 2020 03:02:19: end of X-cor INFO @ Tue, 30 Jun 2020 03:02:19: #2 finished! INFO @ Tue, 30 Jun 2020 03:02:19: #2 predicted fragment length is 62 bps INFO @ Tue, 30 Jun 2020 03:02:19: #2 alternative fragment length(s) may be 2,62,531,544 bps INFO @ Tue, 30 Jun 2020 03:02:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.05_model.r WARNING @ Tue, 30 Jun 2020 03:02:19: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:02:19: #2 You may need to consider one of the other alternative d(s): 2,62,531,544 WARNING @ Tue, 30 Jun 2020 03:02:19: #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 03:02:19: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:02:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:02:20: 16000000 INFO @ Tue, 30 Jun 2020 03:02:22: 12000000 INFO @ Tue, 30 Jun 2020 03:02:27: 17000000 INFO @ Tue, 30 Jun 2020 03:02:28: 13000000 INFO @ Tue, 30 Jun 2020 03:02:34: 18000000 INFO @ Tue, 30 Jun 2020 03:02:35: 14000000 INFO @ Tue, 30 Jun 2020 03:02:41: 19000000 INFO @ Tue, 30 Jun 2020 03:02:41: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:02:48: 16000000 INFO @ Tue, 30 Jun 2020 03:02:48: 20000000 INFO @ Tue, 30 Jun 2020 03:02:49: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:02:49: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:02:49: #1 total tags in treatment: 20132956 INFO @ Tue, 30 Jun 2020 03:02:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:02:49: #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 03:02:50: #1 tags after filtering in treatment: 20132953 INFO @ Tue, 30 Jun 2020 03:02:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:02:50: #1 finished! INFO @ Tue, 30 Jun 2020 03:02:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:02:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:02:51: #2 number of paired peaks: 110 WARNING @ Tue, 30 Jun 2020 03:02:51: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Tue, 30 Jun 2020 03:02:51: start model_add_line... INFO @ Tue, 30 Jun 2020 03:02:51: start X-correlation... INFO @ Tue, 30 Jun 2020 03:02:51: end of X-cor INFO @ Tue, 30 Jun 2020 03:02:51: #2 finished! INFO @ Tue, 30 Jun 2020 03:02:51: #2 predicted fragment length is 62 bps INFO @ Tue, 30 Jun 2020 03:02:51: #2 alternative fragment length(s) may be 2,62,531,544 bps INFO @ Tue, 30 Jun 2020 03:02:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.10_model.r WARNING @ Tue, 30 Jun 2020 03:02:51: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:02:51: #2 You may need to consider one of the other alternative d(s): 2,62,531,544 WARNING @ Tue, 30 Jun 2020 03:02:51: #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 03:02:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:02:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:02:54: 17000000 INFO @ Tue, 30 Jun 2020 03:02:59: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:03:00: 18000000 INFO @ Tue, 30 Jun 2020 03:03:07: 19000000 INFO @ Tue, 30 Jun 2020 03:03:14: 20000000 INFO @ Tue, 30 Jun 2020 03:03:15: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:03:15: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:03:15: #1 total tags in treatment: 20132956 INFO @ Tue, 30 Jun 2020 03:03:15: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:03:15: #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 03:03:15: #1 tags after filtering in treatment: 20132953 INFO @ Tue, 30 Jun 2020 03:03:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:03:15: #1 finished! INFO @ Tue, 30 Jun 2020 03:03:15: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:03:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:03:17: #2 number of paired peaks: 110 WARNING @ Tue, 30 Jun 2020 03:03:17: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Tue, 30 Jun 2020 03:03:17: start model_add_line... INFO @ Tue, 30 Jun 2020 03:03:17: start X-correlation... INFO @ Tue, 30 Jun 2020 03:03:17: end of X-cor INFO @ Tue, 30 Jun 2020 03:03:17: #2 finished! INFO @ Tue, 30 Jun 2020 03:03:17: #2 predicted fragment length is 62 bps INFO @ Tue, 30 Jun 2020 03:03:17: #2 alternative fragment length(s) may be 2,62,531,544 bps INFO @ Tue, 30 Jun 2020 03:03:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.20_model.r WARNING @ Tue, 30 Jun 2020 03:03:17: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:03:17: #2 You may need to consider one of the other alternative d(s): 2,62,531,544 WARNING @ Tue, 30 Jun 2020 03:03:17: #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 03:03:17: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:03:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:03:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:03:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:03:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.05_summits.bed INFO @ Tue, 30 Jun 2020 03:03:21: Done! pass1 - making usageList (306 chroms): 1 millis pass2 - checking and writing primary data (830 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:03:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:03:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:03:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:03:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.10_summits.bed INFO @ Tue, 30 Jun 2020 03:03:54: Done! pass1 - making usageList (172 chroms): 1 millis pass2 - checking and writing primary data (423 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:03:58: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:04:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:04:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:04:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343136/SRX5343136.20_summits.bed INFO @ Tue, 30 Jun 2020 03:04:19: Done! pass1 - making usageList (106 chroms): 1 millis pass2 - checking and writing primary data (233 records, 4 fields): 5 millis CompletedMACS2peakCalling