Job ID = 6455456 SRX = SRX287801 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:03:40 prefetch.2.10.7: 1) Downloading 'SRR869990'... 2020-06-21T10:03:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:06:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:06:06 prefetch.2.10.7: 1) 'SRR869990' was downloaded successfully Read 21266404 spots for SRR869990/SRR869990.sra Written 21266404 spots for SRR869990/SRR869990.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: 00:06:10 21266404 reads; of these: 21266404 (100.00%) were unpaired; of these: 1611492 (7.58%) aligned 0 times 13447349 (63.23%) aligned exactly 1 time 6207563 (29.19%) aligned >1 times 92.42% overall alignment rate Time searching: 00:06:10 Overall time: 00:06:10 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] 4582645 / 19654912 = 0.2332 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 19:18:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.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 19:18:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:18:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:18:42: 1000000 INFO @ Sun, 21 Jun 2020 19:18:48: 2000000 INFO @ Sun, 21 Jun 2020 19:18:54: 3000000 INFO @ Sun, 21 Jun 2020 19:19:00: 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 19:19:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.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 19:19:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:19:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:19:06: 5000000 INFO @ Sun, 21 Jun 2020 19:19:13: 1000000 INFO @ Sun, 21 Jun 2020 19:19:13: 6000000 INFO @ Sun, 21 Jun 2020 19:19:20: 2000000 INFO @ Sun, 21 Jun 2020 19:19:20: 7000000 INFO @ Sun, 21 Jun 2020 19:19:27: 8000000 INFO @ Sun, 21 Jun 2020 19:19:28: 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 @ Sun, 21 Jun 2020 19:19:34: 9000000 INFO @ Sun, 21 Jun 2020 19:19:35: 4000000 INFO @ Sun, 21 Jun 2020 19:19:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.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 19:19:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:19:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:19:42: 10000000 INFO @ Sun, 21 Jun 2020 19:19:42: 5000000 INFO @ Sun, 21 Jun 2020 19:19:43: 1000000 INFO @ Sun, 21 Jun 2020 19:19:49: 11000000 INFO @ Sun, 21 Jun 2020 19:19:50: 6000000 INFO @ Sun, 21 Jun 2020 19:19:51: 2000000 INFO @ Sun, 21 Jun 2020 19:19:57: 12000000 INFO @ Sun, 21 Jun 2020 19:19:58: 7000000 INFO @ Sun, 21 Jun 2020 19:19:58: 3000000 INFO @ Sun, 21 Jun 2020 19:20:05: 13000000 INFO @ Sun, 21 Jun 2020 19:20:06: 8000000 INFO @ Sun, 21 Jun 2020 19:20:06: 4000000 INFO @ Sun, 21 Jun 2020 19:20:13: 14000000 INFO @ Sun, 21 Jun 2020 19:20:13: 5000000 INFO @ Sun, 21 Jun 2020 19:20:13: 9000000 INFO @ Sun, 21 Jun 2020 19:20:20: 15000000 INFO @ Sun, 21 Jun 2020 19:20:20: 6000000 INFO @ Sun, 21 Jun 2020 19:20:21: 10000000 INFO @ Sun, 21 Jun 2020 19:20:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:20:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:20:21: #1 total tags in treatment: 15072267 INFO @ Sun, 21 Jun 2020 19:20:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:20:21: #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 19:20:21: #1 tags after filtering in treatment: 15072267 INFO @ Sun, 21 Jun 2020 19:20:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:20:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:20:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:20:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:20:22: #2 number of paired peaks: 747 WARNING @ Sun, 21 Jun 2020 19:20:22: Fewer paired peaks (747) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 747 pairs to build model! INFO @ Sun, 21 Jun 2020 19:20:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:20:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:20:23: end of X-cor INFO @ Sun, 21 Jun 2020 19:20:23: #2 finished! INFO @ Sun, 21 Jun 2020 19:20:23: #2 predicted fragment length is 36 bps INFO @ Sun, 21 Jun 2020 19:20:23: #2 alternative fragment length(s) may be 3,36 bps INFO @ Sun, 21 Jun 2020 19:20:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.05_model.r WARNING @ Sun, 21 Jun 2020 19:20:23: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:20:23: #2 You may need to consider one of the other alternative d(s): 3,36 WARNING @ Sun, 21 Jun 2020 19:20:23: #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 19:20:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:20:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:20:28: 7000000 INFO @ Sun, 21 Jun 2020 19:20:28: 11000000 INFO @ Sun, 21 Jun 2020 19:20:35: 8000000 INFO @ Sun, 21 Jun 2020 19:20:36: 12000000 INFO @ Sun, 21 Jun 2020 19:20:42: 9000000 INFO @ Sun, 21 Jun 2020 19:20:44: 13000000 INFO @ Sun, 21 Jun 2020 19:20:49: 10000000 INFO @ Sun, 21 Jun 2020 19:20:51: 14000000 INFO @ Sun, 21 Jun 2020 19:20:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:20:56: 11000000 INFO @ Sun, 21 Jun 2020 19:20:59: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:20:59: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:20:59: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:20:59: #1 total tags in treatment: 15072267 INFO @ Sun, 21 Jun 2020 19:20:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:20:59: #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 19:21:00: #1 tags after filtering in treatment: 15072267 INFO @ Sun, 21 Jun 2020 19:21:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:21:00: #1 finished! INFO @ Sun, 21 Jun 2020 19:21:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:21:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:21:01: #2 number of paired peaks: 747 WARNING @ Sun, 21 Jun 2020 19:21:01: Fewer paired peaks (747) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 747 pairs to build model! INFO @ Sun, 21 Jun 2020 19:21:01: start model_add_line... INFO @ Sun, 21 Jun 2020 19:21:01: start X-correlation... INFO @ Sun, 21 Jun 2020 19:21:01: end of X-cor INFO @ Sun, 21 Jun 2020 19:21:01: #2 finished! INFO @ Sun, 21 Jun 2020 19:21:01: #2 predicted fragment length is 36 bps INFO @ Sun, 21 Jun 2020 19:21:01: #2 alternative fragment length(s) may be 3,36 bps INFO @ Sun, 21 Jun 2020 19:21:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.10_model.r WARNING @ Sun, 21 Jun 2020 19:21:01: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:21:01: #2 You may need to consider one of the other alternative d(s): 3,36 WARNING @ Sun, 21 Jun 2020 19:21:01: #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 19:21:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:21:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:21:03: 12000000 INFO @ Sun, 21 Jun 2020 19:21:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:21:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:21:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.05_summits.bed INFO @ Sun, 21 Jun 2020 19:21:07: Done! pass1 - making usageList (652 chroms): 1 millis pass2 - checking and writing primary data (2446 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:21:09: 13000000 INFO @ Sun, 21 Jun 2020 19:21:15: 14000000 INFO @ Sun, 21 Jun 2020 19:21:21: 15000000 INFO @ Sun, 21 Jun 2020 19:21:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:21:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:21:22: #1 total tags in treatment: 15072267 INFO @ Sun, 21 Jun 2020 19:21:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:21:22: #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 19:21:22: #1 tags after filtering in treatment: 15072267 INFO @ Sun, 21 Jun 2020 19:21:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:21:22: #1 finished! INFO @ Sun, 21 Jun 2020 19:21:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:21:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:21:24: #2 number of paired peaks: 747 WARNING @ Sun, 21 Jun 2020 19:21:24: Fewer paired peaks (747) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 747 pairs to build model! INFO @ Sun, 21 Jun 2020 19:21:24: start model_add_line... INFO @ Sun, 21 Jun 2020 19:21:24: start X-correlation... INFO @ Sun, 21 Jun 2020 19:21:24: end of X-cor INFO @ Sun, 21 Jun 2020 19:21:24: #2 finished! INFO @ Sun, 21 Jun 2020 19:21:24: #2 predicted fragment length is 36 bps INFO @ Sun, 21 Jun 2020 19:21:24: #2 alternative fragment length(s) may be 3,36 bps INFO @ Sun, 21 Jun 2020 19:21:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.20_model.r WARNING @ Sun, 21 Jun 2020 19:21:24: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:21:24: #2 You may need to consider one of the other alternative d(s): 3,36 WARNING @ Sun, 21 Jun 2020 19:21:24: #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 19:21:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:21:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:21:29: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:21:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:21:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:21:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.10_summits.bed INFO @ Sun, 21 Jun 2020 19:21:43: Done! pass1 - making usageList (510 chroms): 1 millis pass2 - checking and writing primary data (1970 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:21:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:22:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:22:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:22:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287801/SRX287801.20_summits.bed INFO @ Sun, 21 Jun 2020 19:22:05: Done! pass1 - making usageList (361 chroms): 1 millis pass2 - checking and writing primary data (863 records, 4 fields): 12 millis CompletedMACS2peakCalling