Job ID = 6455005 SRX = SRX2618551 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:35:40 prefetch.2.10.7: 1) Downloading 'SRR5319105'... 2020-06-21T09:35:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:39:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:39:08 prefetch.2.10.7: 1) 'SRR5319105' was downloaded successfully 2020-06-21T09:39:08 prefetch.2.10.7: 'SRR5319105' has 0 unresolved dependencies Read 21538677 spots for SRR5319105/SRR5319105.sra Written 21538677 spots for SRR5319105/SRR5319105.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: 00:05:21 21538677 reads; of these: 21538677 (100.00%) were unpaired; of these: 2021607 (9.39%) aligned 0 times 14711619 (68.30%) aligned exactly 1 time 4805451 (22.31%) aligned >1 times 90.61% overall alignment rate Time searching: 00:05:22 Overall time: 00:05:22 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] 2202738 / 19517070 = 0.1129 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 18:51:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.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 18:51:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:23: 1000000 INFO @ Sun, 21 Jun 2020 18:51:27: 2000000 INFO @ Sun, 21 Jun 2020 18:51:32: 3000000 INFO @ Sun, 21 Jun 2020 18:51:37: 4000000 INFO @ Sun, 21 Jun 2020 18:51:41: 5000000 INFO @ Sun, 21 Jun 2020 18:51:46: 6000000 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 18:51:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.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 18:51:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:50: 7000000 INFO @ Sun, 21 Jun 2020 18:51:53: 1000000 INFO @ Sun, 21 Jun 2020 18:51:55: 8000000 INFO @ Sun, 21 Jun 2020 18:51:57: 2000000 INFO @ Sun, 21 Jun 2020 18:52:00: 9000000 INFO @ Sun, 21 Jun 2020 18:52:02: 3000000 INFO @ Sun, 21 Jun 2020 18:52:04: 10000000 INFO @ Sun, 21 Jun 2020 18:52:07: 4000000 INFO @ Sun, 21 Jun 2020 18:52:09: 11000000 INFO @ Sun, 21 Jun 2020 18:52:12: 5000000 INFO @ Sun, 21 Jun 2020 18:52:14: 12000000 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 18:52:16: 6000000 INFO @ Sun, 21 Jun 2020 18:52:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.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 18:52:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:52:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:52:18: 13000000 INFO @ Sun, 21 Jun 2020 18:52:21: 7000000 INFO @ Sun, 21 Jun 2020 18:52:23: 1000000 INFO @ Sun, 21 Jun 2020 18:52:23: 14000000 INFO @ Sun, 21 Jun 2020 18:52:26: 8000000 INFO @ Sun, 21 Jun 2020 18:52:27: 2000000 INFO @ Sun, 21 Jun 2020 18:52:28: 15000000 INFO @ Sun, 21 Jun 2020 18:52:30: 9000000 INFO @ Sun, 21 Jun 2020 18:52:32: 3000000 INFO @ Sun, 21 Jun 2020 18:52:33: 16000000 INFO @ Sun, 21 Jun 2020 18:52:35: 10000000 INFO @ Sun, 21 Jun 2020 18:52:37: 4000000 INFO @ Sun, 21 Jun 2020 18:52:38: 17000000 INFO @ Sun, 21 Jun 2020 18:52:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:52:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:52:39: #1 total tags in treatment: 17314332 INFO @ Sun, 21 Jun 2020 18:52:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:39: #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 18:52:40: 11000000 INFO @ Sun, 21 Jun 2020 18:52:40: #1 tags after filtering in treatment: 17314332 INFO @ Sun, 21 Jun 2020 18:52:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:40: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:41: #2 number of paired peaks: 952 WARNING @ Sun, 21 Jun 2020 18:52:41: Fewer paired peaks (952) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 952 pairs to build model! INFO @ Sun, 21 Jun 2020 18:52:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:41: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:41: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 18:52:41: #2 alternative fragment length(s) may be 4,59 bps INFO @ Sun, 21 Jun 2020 18:52:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.05_model.r WARNING @ Sun, 21 Jun 2020 18:52:41: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:52:41: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Sun, 21 Jun 2020 18:52:41: #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 18:52:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:52:42: 5000000 INFO @ Sun, 21 Jun 2020 18:52:44: 12000000 INFO @ Sun, 21 Jun 2020 18:52:46: 6000000 INFO @ Sun, 21 Jun 2020 18:52:49: 13000000 INFO @ Sun, 21 Jun 2020 18:52:51: 7000000 INFO @ Sun, 21 Jun 2020 18:52:54: 14000000 INFO @ Sun, 21 Jun 2020 18:52:56: 8000000 INFO @ Sun, 21 Jun 2020 18:52:59: 15000000 INFO @ Sun, 21 Jun 2020 18:53:00: 9000000 INFO @ Sun, 21 Jun 2020 18:53:04: 16000000 INFO @ Sun, 21 Jun 2020 18:53:05: 10000000 INFO @ Sun, 21 Jun 2020 18:53:08: 17000000 INFO @ Sun, 21 Jun 2020 18:53:10: 11000000 INFO @ Sun, 21 Jun 2020 18:53:10: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:53:10: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:53:10: #1 total tags in treatment: 17314332 INFO @ Sun, 21 Jun 2020 18:53:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:53:10: #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 18:53:11: #1 tags after filtering in treatment: 17314332 INFO @ Sun, 21 Jun 2020 18:53:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:53:11: #1 finished! INFO @ Sun, 21 Jun 2020 18:53:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:53:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:53:12: #2 number of paired peaks: 952 WARNING @ Sun, 21 Jun 2020 18:53:12: Fewer paired peaks (952) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 952 pairs to build model! INFO @ Sun, 21 Jun 2020 18:53:12: start model_add_line... INFO @ Sun, 21 Jun 2020 18:53:12: start X-correlation... INFO @ Sun, 21 Jun 2020 18:53:12: end of X-cor INFO @ Sun, 21 Jun 2020 18:53:12: #2 finished! INFO @ Sun, 21 Jun 2020 18:53:12: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 18:53:12: #2 alternative fragment length(s) may be 4,59 bps INFO @ Sun, 21 Jun 2020 18:53:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.10_model.r WARNING @ Sun, 21 Jun 2020 18:53:12: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:53:12: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Sun, 21 Jun 2020 18:53:12: #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 18:53:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:53:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:53:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:53:14: 12000000 INFO @ Sun, 21 Jun 2020 18:53:19: 13000000 INFO @ Sun, 21 Jun 2020 18:53:24: 14000000 INFO @ Sun, 21 Jun 2020 18:53:29: 15000000 INFO @ Sun, 21 Jun 2020 18:53:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:53:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:53:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.05_summits.bed INFO @ Sun, 21 Jun 2020 18:53:30: Done! pass1 - making usageList (629 chroms): 2 millis pass2 - checking and writing primary data (6184 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:53:33: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:53:38: 17000000 INFO @ Sun, 21 Jun 2020 18:53:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:53:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:53:40: #1 total tags in treatment: 17314332 INFO @ Sun, 21 Jun 2020 18:53:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:53:40: #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 18:53:40: #1 tags after filtering in treatment: 17314332 INFO @ Sun, 21 Jun 2020 18:53:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:53:40: #1 finished! INFO @ Sun, 21 Jun 2020 18:53:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:53:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:53:41: #2 number of paired peaks: 952 WARNING @ Sun, 21 Jun 2020 18:53:41: Fewer paired peaks (952) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 952 pairs to build model! INFO @ Sun, 21 Jun 2020 18:53:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:53:42: start X-correlation... INFO @ Sun, 21 Jun 2020 18:53:42: end of X-cor INFO @ Sun, 21 Jun 2020 18:53:42: #2 finished! INFO @ Sun, 21 Jun 2020 18:53:42: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 18:53:42: #2 alternative fragment length(s) may be 4,59 bps INFO @ Sun, 21 Jun 2020 18:53:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.20_model.r WARNING @ Sun, 21 Jun 2020 18:53:42: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:53:42: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Sun, 21 Jun 2020 18:53:42: #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 18:53:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:53:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:53:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:54:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:54:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:54:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.10_summits.bed INFO @ Sun, 21 Jun 2020 18:54:03: Done! pass1 - making usageList (520 chroms): 1 millis pass2 - checking and writing primary data (3322 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:54:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:54:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:54:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:54:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618551/SRX2618551.20_summits.bed INFO @ Sun, 21 Jun 2020 18:54:30: Done! pass1 - making usageList (421 chroms): 1 millis pass2 - checking and writing primary data (1701 records, 4 fields): 13 millis CompletedMACS2peakCalling