Job ID = 6455722 SRX = SRX288019 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:33:52 prefetch.2.10.7: 1) Downloading 'SRR870208'... 2020-06-21T10:33:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:36:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:36:56 prefetch.2.10.7: 'SRR870208' is valid 2020-06-21T10:36:56 prefetch.2.10.7: 1) 'SRR870208' was downloaded successfully Read 14616808 spots for SRR870208/SRR870208.sra Written 14616808 spots for SRR870208/SRR870208.sra 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: 00:00:01 Multiseed full-index search: 00:04:20 14616808 reads; of these: 14616808 (100.00%) were unpaired; of these: 1026272 (7.02%) aligned 0 times 9725880 (66.54%) aligned exactly 1 time 3864656 (26.44%) aligned >1 times 92.98% overall alignment rate Time searching: 00:04:21 Overall time: 00:04:21 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] 4044869 / 13590536 = 0.2976 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 @ Sun, 21 Jun 2020 19:45:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.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 @ Sun, 21 Jun 2020 19:45:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:45:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:45:39: 1000000 INFO @ Sun, 21 Jun 2020 19:45:45: 2000000 INFO @ Sun, 21 Jun 2020 19:45:51: 3000000 INFO @ Sun, 21 Jun 2020 19:45:57: 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 @ Sun, 21 Jun 2020 19:46:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.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 @ Sun, 21 Jun 2020 19:46:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:46:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:46:03: 5000000 INFO @ Sun, 21 Jun 2020 19:46:09: 6000000 INFO @ Sun, 21 Jun 2020 19:46:10: 1000000 INFO @ Sun, 21 Jun 2020 19:46:16: 7000000 INFO @ Sun, 21 Jun 2020 19:46:17: 2000000 INFO @ Sun, 21 Jun 2020 19:46:24: 8000000 INFO @ Sun, 21 Jun 2020 19:46:24: 3000000 INFO @ Sun, 21 Jun 2020 19:46:30: 9000000 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 @ Sun, 21 Jun 2020 19:46:31: 4000000 INFO @ Sun, 21 Jun 2020 19:46:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.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 @ Sun, 21 Jun 2020 19:46:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:46:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:46:34: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:46:34: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:46:34: #1 total tags in treatment: 9545667 INFO @ Sun, 21 Jun 2020 19:46:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:46:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:46:35: #1 tags after filtering in treatment: 9545660 INFO @ Sun, 21 Jun 2020 19:46:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:46:35: #1 finished! INFO @ Sun, 21 Jun 2020 19:46:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:46:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:46:35: #2 number of paired peaks: 403 WARNING @ Sun, 21 Jun 2020 19:46:35: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Sun, 21 Jun 2020 19:46:35: start model_add_line... INFO @ Sun, 21 Jun 2020 19:46:35: start X-correlation... INFO @ Sun, 21 Jun 2020 19:46:35: end of X-cor INFO @ Sun, 21 Jun 2020 19:46:35: #2 finished! INFO @ Sun, 21 Jun 2020 19:46:35: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 19:46:35: #2 alternative fragment length(s) may be 54 bps INFO @ Sun, 21 Jun 2020 19:46:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.05_model.r WARNING @ Sun, 21 Jun 2020 19:46:35: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:46:35: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sun, 21 Jun 2020 19:46:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:46:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:46:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:46:38: 5000000 INFO @ Sun, 21 Jun 2020 19:46:39: 1000000 INFO @ Sun, 21 Jun 2020 19:46:44: 6000000 INFO @ Sun, 21 Jun 2020 19:46:46: 2000000 INFO @ Sun, 21 Jun 2020 19:46:51: 7000000 INFO @ Sun, 21 Jun 2020 19:46:53: 3000000 INFO @ Sun, 21 Jun 2020 19:46:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:46:58: 8000000 INFO @ Sun, 21 Jun 2020 19:46:59: 4000000 INFO @ Sun, 21 Jun 2020 19:47:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:47:05: 9000000 INFO @ Sun, 21 Jun 2020 19:47:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:47:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.05_summits.bed INFO @ Sun, 21 Jun 2020 19:47:05: Done! pass1 - making usageList (653 chroms): 1 millis pass2 - checking and writing primary data (2240 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:47:06: 5000000 INFO @ Sun, 21 Jun 2020 19:47:08: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:47:08: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:47:08: #1 total tags in treatment: 9545667 INFO @ Sun, 21 Jun 2020 19:47:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:47:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:47:09: #1 tags after filtering in treatment: 9545660 INFO @ Sun, 21 Jun 2020 19:47:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:47:09: #1 finished! INFO @ Sun, 21 Jun 2020 19:47:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:47:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:47:10: #2 number of paired peaks: 403 WARNING @ Sun, 21 Jun 2020 19:47:10: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Sun, 21 Jun 2020 19:47:10: start model_add_line... INFO @ Sun, 21 Jun 2020 19:47:10: start X-correlation... INFO @ Sun, 21 Jun 2020 19:47:10: end of X-cor INFO @ Sun, 21 Jun 2020 19:47:10: #2 finished! INFO @ Sun, 21 Jun 2020 19:47:10: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 19:47:10: #2 alternative fragment length(s) may be 54 bps INFO @ Sun, 21 Jun 2020 19:47:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.10_model.r WARNING @ Sun, 21 Jun 2020 19:47:10: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:47:10: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sun, 21 Jun 2020 19:47:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:47:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:47:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:47:12: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:47:18: 7000000 INFO @ Sun, 21 Jun 2020 19:47:25: 8000000 INFO @ Sun, 21 Jun 2020 19:47:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:47:31: 9000000 INFO @ Sun, 21 Jun 2020 19:47:34: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:47:34: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:47:34: #1 total tags in treatment: 9545667 INFO @ Sun, 21 Jun 2020 19:47:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:47:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:47:35: #1 tags after filtering in treatment: 9545660 INFO @ Sun, 21 Jun 2020 19:47:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:47:35: #1 finished! INFO @ Sun, 21 Jun 2020 19:47:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:47:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:47:35: #2 number of paired peaks: 403 WARNING @ Sun, 21 Jun 2020 19:47:35: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Sun, 21 Jun 2020 19:47:35: start model_add_line... INFO @ Sun, 21 Jun 2020 19:47:36: start X-correlation... INFO @ Sun, 21 Jun 2020 19:47:36: end of X-cor INFO @ Sun, 21 Jun 2020 19:47:36: #2 finished! INFO @ Sun, 21 Jun 2020 19:47:36: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 19:47:36: #2 alternative fragment length(s) may be 54 bps INFO @ Sun, 21 Jun 2020 19:47:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.20_model.r WARNING @ Sun, 21 Jun 2020 19:47:36: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:47:36: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sun, 21 Jun 2020 19:47:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:47:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:47:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:47:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:47:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:47:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.10_summits.bed INFO @ Sun, 21 Jun 2020 19:47:39: Done! pass1 - making usageList (394 chroms): 1 millis pass2 - checking and writing primary data (980 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:47:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:48:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:48:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:48:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288019/SRX288019.20_summits.bed INFO @ Sun, 21 Jun 2020 19:48:04: Done! pass1 - making usageList (189 chroms): 0 millis pass2 - checking and writing primary data (383 records, 4 fields): 7 millis CompletedMACS2peakCalling