Job ID = 6627108 SRX = SRX7780062 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: 00:06:40 25736001 reads; of these: 25736001 (100.00%) were unpaired; of these: 3139320 (12.20%) aligned 0 times 16159161 (62.79%) aligned exactly 1 time 6437520 (25.01%) aligned >1 times 87.80% overall alignment rate Time searching: 00:06:40 Overall time: 00:06:40 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] 5541705 / 22596681 = 0.2452 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, 14 Jul 2020 10:07:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.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, 14 Jul 2020 10:07:07: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:07:07: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:07:18: 1000000 INFO @ Tue, 14 Jul 2020 10:07:29: 2000000 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, 14 Jul 2020 10:07:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.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, 14 Jul 2020 10:07:37: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:07:37: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:07:39: 3000000 INFO @ Tue, 14 Jul 2020 10:07:45: 1000000 INFO @ Tue, 14 Jul 2020 10:07:50: 4000000 INFO @ Tue, 14 Jul 2020 10:07:54: 2000000 INFO @ Tue, 14 Jul 2020 10:08:01: 5000000 INFO @ Tue, 14 Jul 2020 10:08:02: 3000000 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, 14 Jul 2020 10:08:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.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, 14 Jul 2020 10:08:07: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:08:07: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:08:10: 4000000 INFO @ Tue, 14 Jul 2020 10:08:12: 6000000 INFO @ Tue, 14 Jul 2020 10:08:18: 1000000 INFO @ Tue, 14 Jul 2020 10:08:19: 5000000 INFO @ Tue, 14 Jul 2020 10:08:23: 7000000 INFO @ Tue, 14 Jul 2020 10:08:27: 6000000 INFO @ Tue, 14 Jul 2020 10:08:29: 2000000 INFO @ Tue, 14 Jul 2020 10:08:34: 8000000 INFO @ Tue, 14 Jul 2020 10:08:36: 7000000 INFO @ Tue, 14 Jul 2020 10:08:41: 3000000 INFO @ Tue, 14 Jul 2020 10:08:44: 9000000 INFO @ Tue, 14 Jul 2020 10:08:45: 8000000 INFO @ Tue, 14 Jul 2020 10:08:52: 4000000 INFO @ Tue, 14 Jul 2020 10:08:53: 9000000 INFO @ Tue, 14 Jul 2020 10:08:55: 10000000 INFO @ Tue, 14 Jul 2020 10:09:02: 10000000 INFO @ Tue, 14 Jul 2020 10:09:03: 5000000 INFO @ Tue, 14 Jul 2020 10:09:06: 11000000 INFO @ Tue, 14 Jul 2020 10:09:11: 11000000 INFO @ Tue, 14 Jul 2020 10:09:15: 6000000 INFO @ Tue, 14 Jul 2020 10:09:17: 12000000 INFO @ Tue, 14 Jul 2020 10:09:20: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:09:26: 7000000 INFO @ Tue, 14 Jul 2020 10:09:28: 13000000 INFO @ Tue, 14 Jul 2020 10:09:28: 13000000 INFO @ Tue, 14 Jul 2020 10:09:37: 8000000 INFO @ Tue, 14 Jul 2020 10:09:38: 14000000 INFO @ Tue, 14 Jul 2020 10:09:40: 14000000 INFO @ Tue, 14 Jul 2020 10:09:47: 15000000 INFO @ Tue, 14 Jul 2020 10:09:48: 9000000 INFO @ Tue, 14 Jul 2020 10:09:51: 15000000 INFO @ Tue, 14 Jul 2020 10:09:55: 16000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:09:59: 10000000 INFO @ Tue, 14 Jul 2020 10:10:02: 16000000 INFO @ Tue, 14 Jul 2020 10:10:04: 17000000 INFO @ Tue, 14 Jul 2020 10:10:05: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 10:10:05: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 10:10:05: #1 total tags in treatment: 17054976 INFO @ Tue, 14 Jul 2020 10:10:05: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:10:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:10:05: #1 tags after filtering in treatment: 17054921 INFO @ Tue, 14 Jul 2020 10:10:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:10:05: #1 finished! INFO @ Tue, 14 Jul 2020 10:10:05: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:10:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:10:06: #2 number of paired peaks: 114 WARNING @ Tue, 14 Jul 2020 10:10:06: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Tue, 14 Jul 2020 10:10:06: start model_add_line... INFO @ Tue, 14 Jul 2020 10:10:06: start X-correlation... INFO @ Tue, 14 Jul 2020 10:10:06: end of X-cor INFO @ Tue, 14 Jul 2020 10:10:06: #2 finished! INFO @ Tue, 14 Jul 2020 10:10:06: #2 predicted fragment length is 44 bps INFO @ Tue, 14 Jul 2020 10:10:06: #2 alternative fragment length(s) may be 18,44,91,445,492,524,570 bps INFO @ Tue, 14 Jul 2020 10:10:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.10_model.r WARNING @ Tue, 14 Jul 2020 10:10:06: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:10:06: #2 You may need to consider one of the other alternative d(s): 18,44,91,445,492,524,570 WARNING @ Tue, 14 Jul 2020 10:10:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:10:06: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:10:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:10:09: 11000000 INFO @ Tue, 14 Jul 2020 10:10:13: 17000000 INFO @ Tue, 14 Jul 2020 10:10:14: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 10:10:14: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 10:10:14: #1 total tags in treatment: 17054976 INFO @ Tue, 14 Jul 2020 10:10:14: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:10:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:10:14: #1 tags after filtering in treatment: 17054921 INFO @ Tue, 14 Jul 2020 10:10:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:10:14: #1 finished! INFO @ Tue, 14 Jul 2020 10:10:14: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:10:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:10:15: #2 number of paired peaks: 114 WARNING @ Tue, 14 Jul 2020 10:10:15: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Tue, 14 Jul 2020 10:10:15: start model_add_line... INFO @ Tue, 14 Jul 2020 10:10:15: start X-correlation... INFO @ Tue, 14 Jul 2020 10:10:15: end of X-cor INFO @ Tue, 14 Jul 2020 10:10:15: #2 finished! INFO @ Tue, 14 Jul 2020 10:10:15: #2 predicted fragment length is 44 bps INFO @ Tue, 14 Jul 2020 10:10:15: #2 alternative fragment length(s) may be 18,44,91,445,492,524,570 bps INFO @ Tue, 14 Jul 2020 10:10:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.05_model.r WARNING @ Tue, 14 Jul 2020 10:10:15: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:10:15: #2 You may need to consider one of the other alternative d(s): 18,44,91,445,492,524,570 WARNING @ Tue, 14 Jul 2020 10:10:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:10:15: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:10:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:10:20: 12000000 INFO @ Tue, 14 Jul 2020 10:10:30: 13000000 INFO @ Tue, 14 Jul 2020 10:10:38: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:10:41: 14000000 INFO @ Tue, 14 Jul 2020 10:10:48: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:10:52: 15000000 INFO @ Tue, 14 Jul 2020 10:10:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:10:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:10:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.10_summits.bed INFO @ Tue, 14 Jul 2020 10:10:53: Done! pass1 - making usageList (182 chroms): 2 millis pass2 - checking and writing primary data (392 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:11:02: 16000000 INFO @ Tue, 14 Jul 2020 10:11:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:11:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:11:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.05_summits.bed INFO @ Tue, 14 Jul 2020 10:11:05: Done! pass1 - making usageList (476 chroms): 1 millis pass2 - checking and writing primary data (1878 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:11:13: 17000000 INFO @ Tue, 14 Jul 2020 10:11:14: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 10:11:14: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 10:11:14: #1 total tags in treatment: 17054976 INFO @ Tue, 14 Jul 2020 10:11:14: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:11:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:11:15: #1 tags after filtering in treatment: 17054921 INFO @ Tue, 14 Jul 2020 10:11:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:11:15: #1 finished! INFO @ Tue, 14 Jul 2020 10:11:15: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:11:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:11:16: #2 number of paired peaks: 114 WARNING @ Tue, 14 Jul 2020 10:11:16: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Tue, 14 Jul 2020 10:11:16: start model_add_line... INFO @ Tue, 14 Jul 2020 10:11:16: start X-correlation... INFO @ Tue, 14 Jul 2020 10:11:16: end of X-cor INFO @ Tue, 14 Jul 2020 10:11:16: #2 finished! INFO @ Tue, 14 Jul 2020 10:11:16: #2 predicted fragment length is 44 bps INFO @ Tue, 14 Jul 2020 10:11:16: #2 alternative fragment length(s) may be 18,44,91,445,492,524,570 bps INFO @ Tue, 14 Jul 2020 10:11:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.20_model.r WARNING @ Tue, 14 Jul 2020 10:11:16: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:11:16: #2 You may need to consider one of the other alternative d(s): 18,44,91,445,492,524,570 WARNING @ Tue, 14 Jul 2020 10:11:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:11:16: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:11:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:11:49: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:12:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:12:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:12:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7780062/SRX7780062.20_summits.bed INFO @ Tue, 14 Jul 2020 10:12:05: Done! pass1 - making usageList (53 chroms): 0 millis pass2 - checking and writing primary data (92 records, 4 fields): 5 millis CompletedMACS2peakCalling