Job ID = 6453272 SRX = SRX110786 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:06:23 prefetch.2.10.7: 1) Downloading 'SRR388368'... 2020-06-21T08:06:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:13:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:13:55 prefetch.2.10.7: 1) 'SRR388368' was downloaded successfully Read 32467660 spots for SRR388368/SRR388368.sra Written 32467660 spots for SRR388368/SRR388368.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: 00:00:00 Multiseed full-index search: 00:06:42 32467660 reads; of these: 32467660 (100.00%) were unpaired; of these: 3276292 (10.09%) aligned 0 times 24379539 (75.09%) aligned exactly 1 time 4811829 (14.82%) aligned >1 times 89.91% overall alignment rate Time searching: 00:06:42 Overall time: 00:06:42 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] 7447743 / 29191368 = 0.2551 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 17:28:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.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 17:28:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:28:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:28:58: 1000000 INFO @ Sun, 21 Jun 2020 17:29:04: 2000000 INFO @ Sun, 21 Jun 2020 17:29:10: 3000000 INFO @ Sun, 21 Jun 2020 17:29:16: 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 17:29:21: 5000000 INFO @ Sun, 21 Jun 2020 17:29:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.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 17:29:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:29:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:29:27: 6000000 INFO @ Sun, 21 Jun 2020 17:29:28: 1000000 INFO @ Sun, 21 Jun 2020 17:29:33: 7000000 INFO @ Sun, 21 Jun 2020 17:29:34: 2000000 INFO @ Sun, 21 Jun 2020 17:29:39: 3000000 INFO @ Sun, 21 Jun 2020 17:29:39: 8000000 INFO @ Sun, 21 Jun 2020 17:29:45: 4000000 INFO @ Sun, 21 Jun 2020 17:29:45: 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 17:29:50: 5000000 INFO @ Sun, 21 Jun 2020 17:29:52: 10000000 INFO @ Sun, 21 Jun 2020 17:29:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.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 17:29:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:29:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:29:56: 6000000 INFO @ Sun, 21 Jun 2020 17:29:58: 11000000 INFO @ Sun, 21 Jun 2020 17:29:58: 1000000 INFO @ Sun, 21 Jun 2020 17:30:02: 7000000 INFO @ Sun, 21 Jun 2020 17:30:04: 12000000 INFO @ Sun, 21 Jun 2020 17:30:04: 2000000 INFO @ Sun, 21 Jun 2020 17:30:07: 8000000 INFO @ Sun, 21 Jun 2020 17:30:10: 13000000 INFO @ Sun, 21 Jun 2020 17:30:10: 3000000 INFO @ Sun, 21 Jun 2020 17:30:13: 9000000 INFO @ Sun, 21 Jun 2020 17:30:16: 14000000 INFO @ Sun, 21 Jun 2020 17:30:16: 4000000 INFO @ Sun, 21 Jun 2020 17:30:19: 10000000 INFO @ Sun, 21 Jun 2020 17:30:22: 15000000 INFO @ Sun, 21 Jun 2020 17:30:22: 5000000 INFO @ Sun, 21 Jun 2020 17:30:24: 11000000 INFO @ Sun, 21 Jun 2020 17:30:28: 6000000 INFO @ Sun, 21 Jun 2020 17:30:28: 16000000 INFO @ Sun, 21 Jun 2020 17:30:30: 12000000 INFO @ Sun, 21 Jun 2020 17:30:34: 7000000 INFO @ Sun, 21 Jun 2020 17:30:34: 17000000 INFO @ Sun, 21 Jun 2020 17:30:35: 13000000 INFO @ Sun, 21 Jun 2020 17:30:39: 8000000 INFO @ Sun, 21 Jun 2020 17:30:40: 18000000 INFO @ Sun, 21 Jun 2020 17:30:41: 14000000 INFO @ Sun, 21 Jun 2020 17:30:45: 9000000 INFO @ Sun, 21 Jun 2020 17:30:46: 19000000 INFO @ Sun, 21 Jun 2020 17:30:46: 15000000 INFO @ Sun, 21 Jun 2020 17:30:50: 10000000 INFO @ Sun, 21 Jun 2020 17:30:52: 16000000 INFO @ Sun, 21 Jun 2020 17:30:52: 20000000 INFO @ Sun, 21 Jun 2020 17:30:56: 11000000 INFO @ Sun, 21 Jun 2020 17:30:57: 17000000 INFO @ Sun, 21 Jun 2020 17:30:58: 21000000 INFO @ Sun, 21 Jun 2020 17:31:01: 12000000 INFO @ Sun, 21 Jun 2020 17:31:03: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:31:03: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:31:03: #1 total tags in treatment: 21743625 INFO @ Sun, 21 Jun 2020 17:31:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:31:03: #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 17:31:03: 18000000 INFO @ Sun, 21 Jun 2020 17:31:03: #1 tags after filtering in treatment: 21743625 INFO @ Sun, 21 Jun 2020 17:31:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:31:03: #1 finished! INFO @ Sun, 21 Jun 2020 17:31:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:31:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:31:05: #2 number of paired peaks: 585 WARNING @ Sun, 21 Jun 2020 17:31:05: Fewer paired peaks (585) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 585 pairs to build model! INFO @ Sun, 21 Jun 2020 17:31:05: start model_add_line... INFO @ Sun, 21 Jun 2020 17:31:05: start X-correlation... INFO @ Sun, 21 Jun 2020 17:31:05: end of X-cor INFO @ Sun, 21 Jun 2020 17:31:05: #2 finished! INFO @ Sun, 21 Jun 2020 17:31:05: #2 predicted fragment length is 73 bps INFO @ Sun, 21 Jun 2020 17:31:05: #2 alternative fragment length(s) may be 2,73 bps INFO @ Sun, 21 Jun 2020 17:31:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.05_model.r WARNING @ Sun, 21 Jun 2020 17:31:05: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:31:05: #2 You may need to consider one of the other alternative d(s): 2,73 WARNING @ Sun, 21 Jun 2020 17:31:05: #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 17:31:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:31:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:31:07: 13000000 INFO @ Sun, 21 Jun 2020 17:31:09: 19000000 INFO @ Sun, 21 Jun 2020 17:31:12: 14000000 INFO @ Sun, 21 Jun 2020 17:31:14: 20000000 INFO @ Sun, 21 Jun 2020 17:31:18: 15000000 INFO @ Sun, 21 Jun 2020 17:31:19: 21000000 INFO @ Sun, 21 Jun 2020 17:31:23: 16000000 INFO @ Sun, 21 Jun 2020 17:31:24: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:31:24: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:31:24: #1 total tags in treatment: 21743625 INFO @ Sun, 21 Jun 2020 17:31:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:31:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:31:24: #1 tags after filtering in treatment: 21743625 INFO @ Sun, 21 Jun 2020 17:31:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:31:24: #1 finished! INFO @ Sun, 21 Jun 2020 17:31:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:31:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:31:26: #2 number of paired peaks: 585 WARNING @ Sun, 21 Jun 2020 17:31:26: Fewer paired peaks (585) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 585 pairs to build model! INFO @ Sun, 21 Jun 2020 17:31:26: start model_add_line... INFO @ Sun, 21 Jun 2020 17:31:26: start X-correlation... INFO @ Sun, 21 Jun 2020 17:31:26: end of X-cor INFO @ Sun, 21 Jun 2020 17:31:26: #2 finished! INFO @ Sun, 21 Jun 2020 17:31:26: #2 predicted fragment length is 73 bps INFO @ Sun, 21 Jun 2020 17:31:26: #2 alternative fragment length(s) may be 2,73 bps INFO @ Sun, 21 Jun 2020 17:31:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.10_model.r WARNING @ Sun, 21 Jun 2020 17:31:26: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:31:26: #2 You may need to consider one of the other alternative d(s): 2,73 WARNING @ Sun, 21 Jun 2020 17:31:26: #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 17:31:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:31:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:31:28: 17000000 INFO @ Sun, 21 Jun 2020 17:31:34: 18000000 INFO @ Sun, 21 Jun 2020 17:31:39: 19000000 INFO @ Sun, 21 Jun 2020 17:31:44: 20000000 INFO @ Sun, 21 Jun 2020 17:31:49: 21000000 INFO @ Sun, 21 Jun 2020 17:31:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:31:53: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:31:53: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:31:53: #1 total tags in treatment: 21743625 INFO @ Sun, 21 Jun 2020 17:31:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:31:53: #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 17:31:53: #1 tags after filtering in treatment: 21743625 INFO @ Sun, 21 Jun 2020 17:31:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:31:53: #1 finished! INFO @ Sun, 21 Jun 2020 17:31:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:31:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:31:55: #2 number of paired peaks: 585 WARNING @ Sun, 21 Jun 2020 17:31:55: Fewer paired peaks (585) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 585 pairs to build model! INFO @ Sun, 21 Jun 2020 17:31:55: start model_add_line... INFO @ Sun, 21 Jun 2020 17:31:55: start X-correlation... INFO @ Sun, 21 Jun 2020 17:31:55: end of X-cor INFO @ Sun, 21 Jun 2020 17:31:55: #2 finished! INFO @ Sun, 21 Jun 2020 17:31:55: #2 predicted fragment length is 73 bps INFO @ Sun, 21 Jun 2020 17:31:55: #2 alternative fragment length(s) may be 2,73 bps INFO @ Sun, 21 Jun 2020 17:31:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.20_model.r WARNING @ Sun, 21 Jun 2020 17:31:55: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:31:55: #2 You may need to consider one of the other alternative d(s): 2,73 WARNING @ Sun, 21 Jun 2020 17:31:55: #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 17:31:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:31:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:32:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:32:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:32:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:32:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.05_summits.bed INFO @ Sun, 21 Jun 2020 17:32:12: Done! pass1 - making usageList (490 chroms): 3 millis pass2 - checking and writing primary data (12361 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:32:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:32:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:32:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.10_summits.bed INFO @ Sun, 21 Jun 2020 17:32:32: Done! pass1 - making usageList (422 chroms): 2 millis pass2 - checking and writing primary data (6977 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:32:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:33:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:33:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:33:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110786/SRX110786.20_summits.bed INFO @ Sun, 21 Jun 2020 17:33:00: Done! pass1 - making usageList (197 chroms): 1 millis pass2 - checking and writing primary data (1479 records, 4 fields): 9 millis CompletedMACS2peakCalling