Job ID = 6509224 SRX = SRX750075 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:29:06 prefetch.2.10.7: 1) Downloading 'SRR1638762'... 2020-06-26T15:29:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:30:22 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:30:22 prefetch.2.10.7: 1) 'SRR1638762' was downloaded successfully Read 14848208 spots for SRR1638762/SRR1638762.sra Written 14848208 spots for SRR1638762/SRR1638762.sra 2020-06-26T15:31:23 prefetch.2.10.7: 1) Downloading 'SRR1638763'... 2020-06-26T15:31:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:33:11 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:33:11 prefetch.2.10.7: 1) 'SRR1638763' was downloaded successfully Read 17300715 spots for SRR1638763/SRR1638763.sra Written 17300715 spots for SRR1638763/SRR1638763.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: 00:12:23 32148923 reads; of these: 32148923 (100.00%) were unpaired; of these: 1875749 (5.83%) aligned 0 times 21712841 (67.54%) aligned exactly 1 time 8560333 (26.63%) aligned >1 times 94.17% overall alignment rate Time searching: 00:12:23 Overall time: 00:12:23 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 16 files... [bam_rmdupse_core] 11857372 / 30273174 = 0.3917 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 @ Sat, 27 Jun 2020 00:54:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.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 @ Sat, 27 Jun 2020 00:54:36: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:54:36: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:54:42: 1000000 INFO @ Sat, 27 Jun 2020 00:54:49: 2000000 INFO @ Sat, 27 Jun 2020 00:54:55: 3000000 INFO @ Sat, 27 Jun 2020 00:55:01: 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 @ Sat, 27 Jun 2020 00:55:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.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 @ Sat, 27 Jun 2020 00:55:06: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:55:06: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:55:08: 5000000 INFO @ Sat, 27 Jun 2020 00:55:14: 1000000 INFO @ Sat, 27 Jun 2020 00:55:15: 6000000 INFO @ Sat, 27 Jun 2020 00:55:23: 2000000 INFO @ Sat, 27 Jun 2020 00:55:23: 7000000 INFO @ Sat, 27 Jun 2020 00:55:30: 8000000 INFO @ Sat, 27 Jun 2020 00:55:31: 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 @ Sat, 27 Jun 2020 00:55:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.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 @ Sat, 27 Jun 2020 00:55:36: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:55:36: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:55:38: 9000000 INFO @ Sat, 27 Jun 2020 00:55:39: 4000000 INFO @ Sat, 27 Jun 2020 00:55:44: 1000000 INFO @ Sat, 27 Jun 2020 00:55:46: 10000000 INFO @ Sat, 27 Jun 2020 00:55:47: 5000000 INFO @ Sat, 27 Jun 2020 00:55:52: 2000000 INFO @ Sat, 27 Jun 2020 00:55:54: 11000000 INFO @ Sat, 27 Jun 2020 00:55:56: 6000000 INFO @ Sat, 27 Jun 2020 00:56:00: 3000000 INFO @ Sat, 27 Jun 2020 00:56:02: 12000000 INFO @ Sat, 27 Jun 2020 00:56:04: 7000000 INFO @ Sat, 27 Jun 2020 00:56:08: 4000000 INFO @ Sat, 27 Jun 2020 00:56:10: 13000000 INFO @ Sat, 27 Jun 2020 00:56:13: 8000000 INFO @ Sat, 27 Jun 2020 00:56:16: 5000000 INFO @ Sat, 27 Jun 2020 00:56:18: 14000000 INFO @ Sat, 27 Jun 2020 00:56:21: 9000000 INFO @ Sat, 27 Jun 2020 00:56:24: 6000000 INFO @ Sat, 27 Jun 2020 00:56:26: 15000000 INFO @ Sat, 27 Jun 2020 00:56:29: 10000000 INFO @ Sat, 27 Jun 2020 00:56:32: 7000000 INFO @ Sat, 27 Jun 2020 00:56:34: 16000000 INFO @ Sat, 27 Jun 2020 00:56:37: 11000000 INFO @ Sat, 27 Jun 2020 00:56:39: 8000000 INFO @ Sat, 27 Jun 2020 00:56:41: 17000000 INFO @ Sat, 27 Jun 2020 00:56:45: 12000000 INFO @ Sat, 27 Jun 2020 00:56:47: 9000000 INFO @ Sat, 27 Jun 2020 00:56:49: 18000000 INFO @ Sat, 27 Jun 2020 00:56:52: #1 tag size is determined as 67 bps INFO @ Sat, 27 Jun 2020 00:56:52: #1 tag size = 67 INFO @ Sat, 27 Jun 2020 00:56:52: #1 total tags in treatment: 18415802 INFO @ Sat, 27 Jun 2020 00:56:52: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:56:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:56:53: #1 tags after filtering in treatment: 18415802 INFO @ Sat, 27 Jun 2020 00:56:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:56:53: #1 finished! INFO @ Sat, 27 Jun 2020 00:56:53: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:56:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:56:53: 13000000 INFO @ Sat, 27 Jun 2020 00:56:54: #2 number of paired peaks: 763 WARNING @ Sat, 27 Jun 2020 00:56:54: Fewer paired peaks (763) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 763 pairs to build model! INFO @ Sat, 27 Jun 2020 00:56:54: start model_add_line... INFO @ Sat, 27 Jun 2020 00:56:54: start X-correlation... INFO @ Sat, 27 Jun 2020 00:56:54: end of X-cor INFO @ Sat, 27 Jun 2020 00:56:54: #2 finished! INFO @ Sat, 27 Jun 2020 00:56:54: #2 predicted fragment length is 50 bps INFO @ Sat, 27 Jun 2020 00:56:54: #2 alternative fragment length(s) may be 2,50 bps INFO @ Sat, 27 Jun 2020 00:56:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.05_model.r WARNING @ Sat, 27 Jun 2020 00:56:54: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:56:54: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Sat, 27 Jun 2020 00:56:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:56:54: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:56:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:56:55: 10000000 INFO @ Sat, 27 Jun 2020 00:57:02: 11000000 INFO @ Sat, 27 Jun 2020 00:57:02: 14000000 INFO @ Sat, 27 Jun 2020 00:57:09: 12000000 INFO @ Sat, 27 Jun 2020 00:57:11: 15000000 INFO @ Sat, 27 Jun 2020 00:57:17: 13000000 INFO @ Sat, 27 Jun 2020 00:57:19: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:57:24: 14000000 INFO @ Sat, 27 Jun 2020 00:57:28: 17000000 INFO @ Sat, 27 Jun 2020 00:57:28: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:57:31: 15000000 INFO @ Sat, 27 Jun 2020 00:57:36: 18000000 INFO @ Sat, 27 Jun 2020 00:57:39: 16000000 INFO @ Sat, 27 Jun 2020 00:57:40: #1 tag size is determined as 67 bps INFO @ Sat, 27 Jun 2020 00:57:40: #1 tag size = 67 INFO @ Sat, 27 Jun 2020 00:57:40: #1 total tags in treatment: 18415802 INFO @ Sat, 27 Jun 2020 00:57:40: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:57:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:57:40: #1 tags after filtering in treatment: 18415802 INFO @ Sat, 27 Jun 2020 00:57:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:57:40: #1 finished! INFO @ Sat, 27 Jun 2020 00:57:40: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:57:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:57:41: #2 number of paired peaks: 763 WARNING @ Sat, 27 Jun 2020 00:57:41: Fewer paired peaks (763) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 763 pairs to build model! INFO @ Sat, 27 Jun 2020 00:57:41: start model_add_line... INFO @ Sat, 27 Jun 2020 00:57:42: start X-correlation... INFO @ Sat, 27 Jun 2020 00:57:42: end of X-cor INFO @ Sat, 27 Jun 2020 00:57:42: #2 finished! INFO @ Sat, 27 Jun 2020 00:57:42: #2 predicted fragment length is 50 bps INFO @ Sat, 27 Jun 2020 00:57:42: #2 alternative fragment length(s) may be 2,50 bps INFO @ Sat, 27 Jun 2020 00:57:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.10_model.r WARNING @ Sat, 27 Jun 2020 00:57:42: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:57:42: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Sat, 27 Jun 2020 00:57:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:57:42: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:57:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:57:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:57:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:57:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.05_summits.bed INFO @ Sat, 27 Jun 2020 00:57:44: Done! pass1 - making usageList (763 chroms): 2 millis pass2 - checking and writing primary data (2898 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:57:46: 17000000 INFO @ Sat, 27 Jun 2020 00:57:52: 18000000 INFO @ Sat, 27 Jun 2020 00:57:55: #1 tag size is determined as 67 bps INFO @ Sat, 27 Jun 2020 00:57:55: #1 tag size = 67 INFO @ Sat, 27 Jun 2020 00:57:55: #1 total tags in treatment: 18415802 INFO @ Sat, 27 Jun 2020 00:57:55: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:57:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:57:56: #1 tags after filtering in treatment: 18415802 INFO @ Sat, 27 Jun 2020 00:57:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:57:56: #1 finished! INFO @ Sat, 27 Jun 2020 00:57:56: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:57:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:57:57: #2 number of paired peaks: 763 WARNING @ Sat, 27 Jun 2020 00:57:57: Fewer paired peaks (763) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 763 pairs to build model! INFO @ Sat, 27 Jun 2020 00:57:57: start model_add_line... INFO @ Sat, 27 Jun 2020 00:57:57: start X-correlation... INFO @ Sat, 27 Jun 2020 00:57:57: end of X-cor INFO @ Sat, 27 Jun 2020 00:57:57: #2 finished! INFO @ Sat, 27 Jun 2020 00:57:57: #2 predicted fragment length is 50 bps INFO @ Sat, 27 Jun 2020 00:57:57: #2 alternative fragment length(s) may be 2,50 bps INFO @ Sat, 27 Jun 2020 00:57:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.20_model.r WARNING @ Sat, 27 Jun 2020 00:57:57: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:57:57: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Sat, 27 Jun 2020 00:57:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:57:57: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:57:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:58:15: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:58:30: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:58:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:58:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:58:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.10_summits.bed INFO @ Sat, 27 Jun 2020 00:58:32: Done! pass1 - making usageList (633 chroms): 1 millis pass2 - checking and writing primary data (2140 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:58:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:58:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:58:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX750075/SRX750075.20_summits.bed INFO @ Sat, 27 Jun 2020 00:58:46: Done! pass1 - making usageList (469 chroms): 1 millis pass2 - checking and writing primary data (1382 records, 4 fields): 14 millis CompletedMACS2peakCalling