Job ID = 6456126 SRX = SRX318799 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:36:44 prefetch.2.10.7: 1) Downloading 'SRR927115'... 2020-06-21T10:36:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:40:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:40:12 prefetch.2.10.7: 1) 'SRR927115' was downloaded successfully Read 19351050 spots for SRR927115/SRR927115.sra Written 19351050 spots for SRR927115/SRR927115.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: 00:05:44 19351050 reads; of these: 19351050 (100.00%) were unpaired; of these: 1132739 (5.85%) aligned 0 times 12586657 (65.04%) aligned exactly 1 time 5631654 (29.10%) aligned >1 times 94.15% overall alignment rate Time searching: 00:05:44 Overall time: 00:05:44 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] 3458941 / 18218311 = 0.1899 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 19:53:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.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 19:53:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:53:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:53:12: 1000000 INFO @ Sun, 21 Jun 2020 19:53:18: 2000000 INFO @ Sun, 21 Jun 2020 19:53:25: 3000000 INFO @ Sun, 21 Jun 2020 19:53:31: 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 19:53:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.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 19:53:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:53:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:53:38: 5000000 INFO @ Sun, 21 Jun 2020 19:53:42: 1000000 INFO @ Sun, 21 Jun 2020 19:53:44: 6000000 INFO @ Sun, 21 Jun 2020 19:53:49: 2000000 INFO @ Sun, 21 Jun 2020 19:53:50: 7000000 INFO @ Sun, 21 Jun 2020 19:53:56: 3000000 INFO @ Sun, 21 Jun 2020 19:53:56: 8000000 INFO @ Sun, 21 Jun 2020 19:54:02: 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 19:54:02: 4000000 INFO @ Sun, 21 Jun 2020 19:54:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.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 19:54:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:54:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:54:08: 10000000 INFO @ Sun, 21 Jun 2020 19:54:10: 5000000 INFO @ Sun, 21 Jun 2020 19:54:12: 1000000 INFO @ Sun, 21 Jun 2020 19:54:13: 11000000 INFO @ Sun, 21 Jun 2020 19:54:17: 6000000 INFO @ Sun, 21 Jun 2020 19:54:19: 2000000 INFO @ Sun, 21 Jun 2020 19:54:19: 12000000 INFO @ Sun, 21 Jun 2020 19:54:24: 7000000 INFO @ Sun, 21 Jun 2020 19:54:26: 13000000 INFO @ Sun, 21 Jun 2020 19:54:26: 3000000 INFO @ Sun, 21 Jun 2020 19:54:31: 8000000 INFO @ Sun, 21 Jun 2020 19:54:32: 14000000 INFO @ Sun, 21 Jun 2020 19:54:33: 4000000 INFO @ Sun, 21 Jun 2020 19:54:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:54:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:54:37: #1 total tags in treatment: 14759370 INFO @ Sun, 21 Jun 2020 19:54:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:54:37: #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 19:54:37: #1 tags after filtering in treatment: 14759370 INFO @ Sun, 21 Jun 2020 19:54:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:54:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:54:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:54:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:54:38: 9000000 INFO @ Sun, 21 Jun 2020 19:54:38: #2 number of paired peaks: 992 WARNING @ Sun, 21 Jun 2020 19:54:38: Fewer paired peaks (992) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 992 pairs to build model! INFO @ Sun, 21 Jun 2020 19:54:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:54:39: start X-correlation... INFO @ Sun, 21 Jun 2020 19:54:39: end of X-cor INFO @ Sun, 21 Jun 2020 19:54:39: #2 finished! INFO @ Sun, 21 Jun 2020 19:54:39: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 19:54:39: #2 alternative fragment length(s) may be 2,47,589 bps INFO @ Sun, 21 Jun 2020 19:54:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.05_model.r WARNING @ Sun, 21 Jun 2020 19:54:39: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:54:39: #2 You may need to consider one of the other alternative d(s): 2,47,589 WARNING @ Sun, 21 Jun 2020 19:54:39: #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 19:54:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:54:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:54:40: 5000000 INFO @ Sun, 21 Jun 2020 19:54:45: 10000000 INFO @ Sun, 21 Jun 2020 19:54:47: 6000000 INFO @ Sun, 21 Jun 2020 19:54:52: 11000000 INFO @ Sun, 21 Jun 2020 19:54:54: 7000000 INFO @ Sun, 21 Jun 2020 19:54:59: 12000000 INFO @ Sun, 21 Jun 2020 19:55:01: 8000000 INFO @ Sun, 21 Jun 2020 19:55:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:55:07: 13000000 INFO @ Sun, 21 Jun 2020 19:55:08: 9000000 INFO @ Sun, 21 Jun 2020 19:55:14: 14000000 INFO @ Sun, 21 Jun 2020 19:55:15: 10000000 INFO @ Sun, 21 Jun 2020 19:55:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:55:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:55:20: #1 total tags in treatment: 14759370 INFO @ Sun, 21 Jun 2020 19:55:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:55:20: #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 19:55:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:55:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:55:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.05_summits.bed INFO @ Sun, 21 Jun 2020 19:55:20: Done! INFO @ Sun, 21 Jun 2020 19:55:21: #1 tags after filtering in treatment: 14759370 INFO @ Sun, 21 Jun 2020 19:55:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:55:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:55:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:55:21: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (613 chroms): 2 millis pass2 - checking and writing primary data (2907 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:55:22: #2 number of paired peaks: 992 WARNING @ Sun, 21 Jun 2020 19:55:22: Fewer paired peaks (992) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 992 pairs to build model! INFO @ Sun, 21 Jun 2020 19:55:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:55:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:55:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:55:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:55:22: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 19:55:22: #2 alternative fragment length(s) may be 2,47,589 bps INFO @ Sun, 21 Jun 2020 19:55:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.10_model.r WARNING @ Sun, 21 Jun 2020 19:55:22: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:55:22: #2 You may need to consider one of the other alternative d(s): 2,47,589 WARNING @ Sun, 21 Jun 2020 19:55:22: #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 19:55:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:55:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:55:22: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:55:29: 12000000 INFO @ Sun, 21 Jun 2020 19:55:36: 13000000 INFO @ Sun, 21 Jun 2020 19:55:42: 14000000 INFO @ Sun, 21 Jun 2020 19:55:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:55:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:55:48: #1 total tags in treatment: 14759370 INFO @ Sun, 21 Jun 2020 19:55:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:55:48: #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 19:55:49: #1 tags after filtering in treatment: 14759370 INFO @ Sun, 21 Jun 2020 19:55:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:55:49: #1 finished! INFO @ Sun, 21 Jun 2020 19:55:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:55:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:55:50: #2 number of paired peaks: 992 WARNING @ Sun, 21 Jun 2020 19:55:50: Fewer paired peaks (992) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 992 pairs to build model! INFO @ Sun, 21 Jun 2020 19:55:50: start model_add_line... INFO @ Sun, 21 Jun 2020 19:55:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:55:50: start X-correlation... INFO @ Sun, 21 Jun 2020 19:55:50: end of X-cor INFO @ Sun, 21 Jun 2020 19:55:50: #2 finished! INFO @ Sun, 21 Jun 2020 19:55:50: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 19:55:50: #2 alternative fragment length(s) may be 2,47,589 bps INFO @ Sun, 21 Jun 2020 19:55:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.20_model.r WARNING @ Sun, 21 Jun 2020 19:55:50: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:55:50: #2 You may need to consider one of the other alternative d(s): 2,47,589 WARNING @ Sun, 21 Jun 2020 19:55:50: #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 19:55:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:55:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:56:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:56:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:56:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.10_summits.bed INFO @ Sun, 21 Jun 2020 19:56:04: Done! pass1 - making usageList (547 chroms): 2 millis pass2 - checking and writing primary data (2090 records, 4 fields): 32 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:56:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:56:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:56:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:56:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318799/SRX318799.20_summits.bed INFO @ Sun, 21 Jun 2020 19:56:32: Done! pass1 - making usageList (323 chroms): 1 millis pass2 - checking and writing primary data (829 records, 4 fields): 20 millis CompletedMACS2peakCalling