Job ID = 6529836 SRX = SRX495294 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 28429556 reads; of these: 28429556 (100.00%) were unpaired; of these: 10381043 (36.51%) aligned 0 times 14128718 (49.70%) aligned exactly 1 time 3919795 (13.79%) aligned >1 times 63.49% 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] 4311598 / 18048513 = 0.2389 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 02:48:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.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 02:48:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:48:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:48:33: 1000000 INFO @ Tue, 30 Jun 2020 02:48:38: 2000000 INFO @ Tue, 30 Jun 2020 02:48:42: 3000000 INFO @ Tue, 30 Jun 2020 02:48:47: 4000000 INFO @ Tue, 30 Jun 2020 02:48:52: 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 02:48:56: 6000000 INFO @ Tue, 30 Jun 2020 02:48:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.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 02:48:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:48:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:49:01: 7000000 INFO @ Tue, 30 Jun 2020 02:49:03: 1000000 INFO @ Tue, 30 Jun 2020 02:49:06: 8000000 INFO @ Tue, 30 Jun 2020 02:49:08: 2000000 INFO @ Tue, 30 Jun 2020 02:49:11: 9000000 INFO @ Tue, 30 Jun 2020 02:49:12: 3000000 INFO @ Tue, 30 Jun 2020 02:49:15: 10000000 INFO @ Tue, 30 Jun 2020 02:49:17: 4000000 INFO @ Tue, 30 Jun 2020 02:49:20: 11000000 INFO @ Tue, 30 Jun 2020 02:49:22: 5000000 INFO @ Tue, 30 Jun 2020 02:49:25: 12000000 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 02:49:27: 6000000 INFO @ Tue, 30 Jun 2020 02:49:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.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 02:49:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:49:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:49:30: 13000000 INFO @ Tue, 30 Jun 2020 02:49:31: 7000000 INFO @ Tue, 30 Jun 2020 02:49:33: 1000000 INFO @ Tue, 30 Jun 2020 02:49:34: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:49:34: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:49:34: #1 total tags in treatment: 13736915 INFO @ Tue, 30 Jun 2020 02:49:34: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:49:34: #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 02:49:34: #1 tags after filtering in treatment: 13736912 INFO @ Tue, 30 Jun 2020 02:49:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:49:34: #1 finished! INFO @ Tue, 30 Jun 2020 02:49:34: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:49:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:49:35: #2 number of paired peaks: 118 WARNING @ Tue, 30 Jun 2020 02:49:35: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Tue, 30 Jun 2020 02:49:35: start model_add_line... INFO @ Tue, 30 Jun 2020 02:49:35: start X-correlation... INFO @ Tue, 30 Jun 2020 02:49:35: end of X-cor INFO @ Tue, 30 Jun 2020 02:49:35: #2 finished! INFO @ Tue, 30 Jun 2020 02:49:35: #2 predicted fragment length is 54 bps INFO @ Tue, 30 Jun 2020 02:49:35: #2 alternative fragment length(s) may be 3,54,436,529,540,583 bps INFO @ Tue, 30 Jun 2020 02:49:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.05_model.r WARNING @ Tue, 30 Jun 2020 02:49:35: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:49:35: #2 You may need to consider one of the other alternative d(s): 3,54,436,529,540,583 WARNING @ Tue, 30 Jun 2020 02:49:35: #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 02:49:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:49:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:49:36: 8000000 INFO @ Tue, 30 Jun 2020 02:49:39: 2000000 INFO @ Tue, 30 Jun 2020 02:49:41: 9000000 INFO @ Tue, 30 Jun 2020 02:49:44: 3000000 INFO @ Tue, 30 Jun 2020 02:49:46: 10000000 INFO @ Tue, 30 Jun 2020 02:49:49: 4000000 INFO @ Tue, 30 Jun 2020 02:49:51: 11000000 INFO @ Tue, 30 Jun 2020 02:49:53: 5000000 INFO @ Tue, 30 Jun 2020 02:49:56: 12000000 INFO @ Tue, 30 Jun 2020 02:49:58: 6000000 INFO @ Tue, 30 Jun 2020 02:50:01: 13000000 INFO @ Tue, 30 Jun 2020 02:50:02: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:50:03: 7000000 INFO @ Tue, 30 Jun 2020 02:50:04: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:50:04: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:50:04: #1 total tags in treatment: 13736915 INFO @ Tue, 30 Jun 2020 02:50:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:50:04: #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 02:50:05: #1 tags after filtering in treatment: 13736912 INFO @ Tue, 30 Jun 2020 02:50:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:50:05: #1 finished! INFO @ Tue, 30 Jun 2020 02:50:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:50:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:50:06: #2 number of paired peaks: 118 WARNING @ Tue, 30 Jun 2020 02:50:06: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Tue, 30 Jun 2020 02:50:06: start model_add_line... INFO @ Tue, 30 Jun 2020 02:50:06: start X-correlation... INFO @ Tue, 30 Jun 2020 02:50:06: end of X-cor INFO @ Tue, 30 Jun 2020 02:50:06: #2 finished! INFO @ Tue, 30 Jun 2020 02:50:06: #2 predicted fragment length is 54 bps INFO @ Tue, 30 Jun 2020 02:50:06: #2 alternative fragment length(s) may be 3,54,436,529,540,583 bps INFO @ Tue, 30 Jun 2020 02:50:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.10_model.r WARNING @ Tue, 30 Jun 2020 02:50:06: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:50:06: #2 You may need to consider one of the other alternative d(s): 3,54,436,529,540,583 WARNING @ Tue, 30 Jun 2020 02:50:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:50:06: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:50:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:50:08: 8000000 INFO @ Tue, 30 Jun 2020 02:50:13: 9000000 INFO @ Tue, 30 Jun 2020 02:50:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:50:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:50:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.05_summits.bed INFO @ Tue, 30 Jun 2020 02:50:14: Done! pass1 - making usageList (340 chroms): 1 millis pass2 - checking and writing primary data (1208 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:50:17: 10000000 INFO @ Tue, 30 Jun 2020 02:50:22: 11000000 INFO @ Tue, 30 Jun 2020 02:50:27: 12000000 INFO @ Tue, 30 Jun 2020 02:50:32: 13000000 INFO @ Tue, 30 Jun 2020 02:50:32: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:50:36: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:50:36: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:50:36: #1 total tags in treatment: 13736915 INFO @ Tue, 30 Jun 2020 02:50:36: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:50:36: #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 02:50:36: #1 tags after filtering in treatment: 13736912 INFO @ Tue, 30 Jun 2020 02:50:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:50:36: #1 finished! INFO @ Tue, 30 Jun 2020 02:50:36: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:50:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:50:37: #2 number of paired peaks: 118 WARNING @ Tue, 30 Jun 2020 02:50:37: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Tue, 30 Jun 2020 02:50:37: start model_add_line... INFO @ Tue, 30 Jun 2020 02:50:37: start X-correlation... INFO @ Tue, 30 Jun 2020 02:50:37: end of X-cor INFO @ Tue, 30 Jun 2020 02:50:37: #2 finished! INFO @ Tue, 30 Jun 2020 02:50:37: #2 predicted fragment length is 54 bps INFO @ Tue, 30 Jun 2020 02:50:37: #2 alternative fragment length(s) may be 3,54,436,529,540,583 bps INFO @ Tue, 30 Jun 2020 02:50:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.20_model.r WARNING @ Tue, 30 Jun 2020 02:50:37: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:50:37: #2 You may need to consider one of the other alternative d(s): 3,54,436,529,540,583 WARNING @ Tue, 30 Jun 2020 02:50:37: #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 02:50:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:50:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:50:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:50:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:50:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.10_summits.bed INFO @ Tue, 30 Jun 2020 02:50:45: Done! pass1 - making usageList (132 chroms): 1 millis pass2 - checking and writing primary data (418 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:51:03: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:51:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:51:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:51:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495294/SRX495294.20_summits.bed INFO @ Tue, 30 Jun 2020 02:51:16: Done! pass1 - making usageList (75 chroms): 1 millis pass2 - checking and writing primary data (139 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。