Job ID = 6453758 SRX = SRX1433401 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:40:02 prefetch.2.10.7: 1) Downloading 'SRR2919817'... 2020-06-21T08:40:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:43:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:43:11 prefetch.2.10.7: 1) 'SRR2919817' was downloaded successfully Read 29185176 spots for SRR2919817/SRR2919817.sra Written 29185176 spots for SRR2919817/SRR2919817.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: 00:06:00 29185176 reads; of these: 29185176 (100.00%) were unpaired; of these: 2902771 (9.95%) aligned 0 times 20184873 (69.16%) aligned exactly 1 time 6097532 (20.89%) aligned >1 times 90.05% overall alignment rate Time searching: 00:06:00 Overall time: 00:06:00 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] 8567230 / 26282405 = 0.3260 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 17:55:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.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 17:55:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:55:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:55:21: 1000000 INFO @ Sun, 21 Jun 2020 17:55:26: 2000000 INFO @ Sun, 21 Jun 2020 17:55:31: 3000000 INFO @ Sun, 21 Jun 2020 17:55:36: 4000000 INFO @ Sun, 21 Jun 2020 17:55:41: 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 @ Sun, 21 Jun 2020 17:55:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.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 17:55:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:55:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:55:47: 6000000 INFO @ Sun, 21 Jun 2020 17:55:51: 1000000 INFO @ Sun, 21 Jun 2020 17:55:52: 7000000 INFO @ Sun, 21 Jun 2020 17:55:57: 2000000 INFO @ Sun, 21 Jun 2020 17:55:58: 8000000 INFO @ Sun, 21 Jun 2020 17:56:03: 3000000 INFO @ Sun, 21 Jun 2020 17:56:04: 9000000 INFO @ Sun, 21 Jun 2020 17:56:09: 4000000 INFO @ Sun, 21 Jun 2020 17:56:10: 10000000 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 17:56:14: 5000000 INFO @ Sun, 21 Jun 2020 17:56:15: 11000000 INFO @ Sun, 21 Jun 2020 17:56:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.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 17:56:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:56:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:56:20: 6000000 INFO @ Sun, 21 Jun 2020 17:56:21: 12000000 INFO @ Sun, 21 Jun 2020 17:56:23: 1000000 INFO @ Sun, 21 Jun 2020 17:56:26: 7000000 INFO @ Sun, 21 Jun 2020 17:56:27: 13000000 INFO @ Sun, 21 Jun 2020 17:56:30: 2000000 INFO @ Sun, 21 Jun 2020 17:56:33: 8000000 INFO @ Sun, 21 Jun 2020 17:56:34: 14000000 INFO @ Sun, 21 Jun 2020 17:56:36: 3000000 INFO @ Sun, 21 Jun 2020 17:56:39: 9000000 INFO @ Sun, 21 Jun 2020 17:56:40: 15000000 INFO @ Sun, 21 Jun 2020 17:56:43: 4000000 INFO @ Sun, 21 Jun 2020 17:56:45: 10000000 INFO @ Sun, 21 Jun 2020 17:56:46: 16000000 INFO @ Sun, 21 Jun 2020 17:56:50: 5000000 INFO @ Sun, 21 Jun 2020 17:56:51: 11000000 INFO @ Sun, 21 Jun 2020 17:56:52: 17000000 INFO @ Sun, 21 Jun 2020 17:56:57: 6000000 INFO @ Sun, 21 Jun 2020 17:56:57: 12000000 INFO @ Sun, 21 Jun 2020 17:56:57: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 17:56:57: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 17:56:57: #1 total tags in treatment: 17715175 INFO @ Sun, 21 Jun 2020 17:56:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:56:57: #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 17:56:58: #1 tags after filtering in treatment: 17715110 INFO @ Sun, 21 Jun 2020 17:56:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:56:58: #1 finished! INFO @ Sun, 21 Jun 2020 17:56:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:56:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:56:59: #2 number of paired peaks: 644 WARNING @ Sun, 21 Jun 2020 17:56:59: Fewer paired peaks (644) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 644 pairs to build model! INFO @ Sun, 21 Jun 2020 17:56:59: start model_add_line... INFO @ Sun, 21 Jun 2020 17:56:59: start X-correlation... INFO @ Sun, 21 Jun 2020 17:56:59: end of X-cor INFO @ Sun, 21 Jun 2020 17:56:59: #2 finished! INFO @ Sun, 21 Jun 2020 17:56:59: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 17:56:59: #2 alternative fragment length(s) may be 3,79,598 bps INFO @ Sun, 21 Jun 2020 17:56:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.05_model.r WARNING @ Sun, 21 Jun 2020 17:56:59: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:56:59: #2 You may need to consider one of the other alternative d(s): 3,79,598 WARNING @ Sun, 21 Jun 2020 17:56:59: #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 17:56:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:56:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:57:03: 13000000 INFO @ Sun, 21 Jun 2020 17:57:03: 7000000 INFO @ Sun, 21 Jun 2020 17:57:09: 14000000 INFO @ Sun, 21 Jun 2020 17:57:10: 8000000 INFO @ Sun, 21 Jun 2020 17:57:15: 15000000 INFO @ Sun, 21 Jun 2020 17:57:16: 9000000 INFO @ Sun, 21 Jun 2020 17:57:21: 16000000 INFO @ Sun, 21 Jun 2020 17:57:23: 10000000 INFO @ Sun, 21 Jun 2020 17:57:27: 17000000 INFO @ Sun, 21 Jun 2020 17:57:30: 11000000 INFO @ Sun, 21 Jun 2020 17:57:32: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 17:57:32: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 17:57:32: #1 total tags in treatment: 17715175 INFO @ Sun, 21 Jun 2020 17:57:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:57:32: #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 17:57:32: #1 tags after filtering in treatment: 17715110 INFO @ Sun, 21 Jun 2020 17:57:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:57:32: #1 finished! INFO @ Sun, 21 Jun 2020 17:57:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:57:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:57:34: #2 number of paired peaks: 644 WARNING @ Sun, 21 Jun 2020 17:57:34: Fewer paired peaks (644) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 644 pairs to build model! INFO @ Sun, 21 Jun 2020 17:57:34: start model_add_line... INFO @ Sun, 21 Jun 2020 17:57:34: start X-correlation... INFO @ Sun, 21 Jun 2020 17:57:34: end of X-cor INFO @ Sun, 21 Jun 2020 17:57:34: #2 finished! INFO @ Sun, 21 Jun 2020 17:57:34: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 17:57:34: #2 alternative fragment length(s) may be 3,79,598 bps INFO @ Sun, 21 Jun 2020 17:57:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.10_model.r WARNING @ Sun, 21 Jun 2020 17:57:34: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:57:34: #2 You may need to consider one of the other alternative d(s): 3,79,598 WARNING @ Sun, 21 Jun 2020 17:57:34: #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 17:57:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:57:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:57:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:57:36: 12000000 INFO @ Sun, 21 Jun 2020 17:57:42: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:57:49: 14000000 INFO @ Sun, 21 Jun 2020 17:57:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:57:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:57:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.05_summits.bed INFO @ Sun, 21 Jun 2020 17:57:54: Done! pass1 - making usageList (462 chroms): 1 millis pass2 - checking and writing primary data (3793 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:57:55: 15000000 INFO @ Sun, 21 Jun 2020 17:58:02: 16000000 INFO @ Sun, 21 Jun 2020 17:58:08: 17000000 INFO @ Sun, 21 Jun 2020 17:58:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:58:13: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 17:58:13: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 17:58:13: #1 total tags in treatment: 17715175 INFO @ Sun, 21 Jun 2020 17:58:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:58:13: #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 17:58:13: #1 tags after filtering in treatment: 17715110 INFO @ Sun, 21 Jun 2020 17:58:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:58:13: #1 finished! INFO @ Sun, 21 Jun 2020 17:58:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:58:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:58:14: #2 number of paired peaks: 644 WARNING @ Sun, 21 Jun 2020 17:58:14: Fewer paired peaks (644) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 644 pairs to build model! INFO @ Sun, 21 Jun 2020 17:58:14: start model_add_line... INFO @ Sun, 21 Jun 2020 17:58:15: start X-correlation... INFO @ Sun, 21 Jun 2020 17:58:15: end of X-cor INFO @ Sun, 21 Jun 2020 17:58:15: #2 finished! INFO @ Sun, 21 Jun 2020 17:58:15: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 17:58:15: #2 alternative fragment length(s) may be 3,79,598 bps INFO @ Sun, 21 Jun 2020 17:58:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.20_model.r WARNING @ Sun, 21 Jun 2020 17:58:15: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:58:15: #2 You may need to consider one of the other alternative d(s): 3,79,598 WARNING @ Sun, 21 Jun 2020 17:58:15: #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 17:58:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:58:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:58:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:58:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:58:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.10_summits.bed INFO @ Sun, 21 Jun 2020 17:58:27: Done! pass1 - making usageList (314 chroms): 1 millis pass2 - checking and writing primary data (1861 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:58:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:59:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:59:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:59:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433401/SRX1433401.20_summits.bed INFO @ Sun, 21 Jun 2020 17:59:07: Done! pass1 - making usageList (159 chroms): 1 millis pass2 - checking and writing primary data (659 records, 4 fields): 6 millis CompletedMACS2peakCalling