Job ID = 6453906 SRX = SRX159165 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:55:04 prefetch.2.10.7: 1) Downloading 'SRR520446'... 2020-06-21T08:55:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:58:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:58:31 prefetch.2.10.7: 1) 'SRR520446' was downloaded successfully Read 26546524 spots for SRR520446/SRR520446.sra Written 26546524 spots for SRR520446/SRR520446.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: 00:06:56 26546524 reads; of these: 26546524 (100.00%) were unpaired; of these: 4721112 (17.78%) aligned 0 times 16173964 (60.93%) aligned exactly 1 time 5651448 (21.29%) aligned >1 times 82.22% overall alignment rate Time searching: 00:06:56 Overall time: 00:06:56 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] 2303275 / 21825412 = 0.1055 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 18:12:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.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 18:12:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:12:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:12:32: 1000000 INFO @ Sun, 21 Jun 2020 18:12:37: 2000000 INFO @ Sun, 21 Jun 2020 18:12:43: 3000000 INFO @ Sun, 21 Jun 2020 18:12:49: 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 18:12:55: 5000000 INFO @ Sun, 21 Jun 2020 18:12:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.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 18:12:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:12:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:13:02: 6000000 INFO @ Sun, 21 Jun 2020 18:13:03: 1000000 INFO @ Sun, 21 Jun 2020 18:13:08: 7000000 INFO @ Sun, 21 Jun 2020 18:13:09: 2000000 INFO @ Sun, 21 Jun 2020 18:13:15: 8000000 INFO @ Sun, 21 Jun 2020 18:13:16: 3000000 INFO @ Sun, 21 Jun 2020 18:13:22: 9000000 INFO @ Sun, 21 Jun 2020 18:13:23: 4000000 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 18:13:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.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 18:13:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:13:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:13:29: 10000000 INFO @ Sun, 21 Jun 2020 18:13:30: 5000000 INFO @ Sun, 21 Jun 2020 18:13:33: 1000000 INFO @ Sun, 21 Jun 2020 18:13:36: 11000000 INFO @ Sun, 21 Jun 2020 18:13:37: 6000000 INFO @ Sun, 21 Jun 2020 18:13:40: 2000000 INFO @ Sun, 21 Jun 2020 18:13:42: 12000000 INFO @ Sun, 21 Jun 2020 18:13:44: 7000000 INFO @ Sun, 21 Jun 2020 18:13:47: 3000000 INFO @ Sun, 21 Jun 2020 18:13:49: 13000000 INFO @ Sun, 21 Jun 2020 18:13:50: 8000000 INFO @ Sun, 21 Jun 2020 18:13:54: 4000000 INFO @ Sun, 21 Jun 2020 18:13:56: 14000000 INFO @ Sun, 21 Jun 2020 18:13:57: 9000000 INFO @ Sun, 21 Jun 2020 18:14:01: 5000000 INFO @ Sun, 21 Jun 2020 18:14:03: 15000000 INFO @ Sun, 21 Jun 2020 18:14:04: 10000000 INFO @ Sun, 21 Jun 2020 18:14:08: 6000000 INFO @ Sun, 21 Jun 2020 18:14:10: 16000000 INFO @ Sun, 21 Jun 2020 18:14:11: 11000000 INFO @ Sun, 21 Jun 2020 18:14:14: 7000000 INFO @ Sun, 21 Jun 2020 18:14:17: 17000000 INFO @ Sun, 21 Jun 2020 18:14:18: 12000000 INFO @ Sun, 21 Jun 2020 18:14:21: 8000000 INFO @ Sun, 21 Jun 2020 18:14:24: 18000000 INFO @ Sun, 21 Jun 2020 18:14:24: 13000000 INFO @ Sun, 21 Jun 2020 18:14:28: 9000000 INFO @ Sun, 21 Jun 2020 18:14:31: 14000000 INFO @ Sun, 21 Jun 2020 18:14:31: 19000000 INFO @ Sun, 21 Jun 2020 18:14:35: 10000000 INFO @ Sun, 21 Jun 2020 18:14:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:14:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:14:35: #1 total tags in treatment: 19522137 INFO @ Sun, 21 Jun 2020 18:14:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:14:35: #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 18:14:36: #1 tags after filtering in treatment: 19522074 INFO @ Sun, 21 Jun 2020 18:14:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:14:36: #1 finished! INFO @ Sun, 21 Jun 2020 18:14:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:14:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:14:37: #2 number of paired peaks: 391 WARNING @ Sun, 21 Jun 2020 18:14:37: Fewer paired peaks (391) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 391 pairs to build model! INFO @ Sun, 21 Jun 2020 18:14:37: start model_add_line... INFO @ Sun, 21 Jun 2020 18:14:37: start X-correlation... INFO @ Sun, 21 Jun 2020 18:14:37: end of X-cor INFO @ Sun, 21 Jun 2020 18:14:37: #2 finished! INFO @ Sun, 21 Jun 2020 18:14:37: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 18:14:37: #2 alternative fragment length(s) may be 3,56 bps INFO @ Sun, 21 Jun 2020 18:14:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.05_model.r WARNING @ Sun, 21 Jun 2020 18:14:37: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:14:37: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Sun, 21 Jun 2020 18:14:37: #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 18:14:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:14:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:14:38: 15000000 INFO @ Sun, 21 Jun 2020 18:14:42: 11000000 INFO @ Sun, 21 Jun 2020 18:14:46: 16000000 INFO @ Sun, 21 Jun 2020 18:14:48: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:14:53: 17000000 INFO @ Sun, 21 Jun 2020 18:14:56: 13000000 INFO @ Sun, 21 Jun 2020 18:15:00: 18000000 INFO @ Sun, 21 Jun 2020 18:15:03: 14000000 INFO @ Sun, 21 Jun 2020 18:15:07: 19000000 INFO @ Sun, 21 Jun 2020 18:15:10: 15000000 INFO @ Sun, 21 Jun 2020 18:15:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:15:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:15:12: #1 total tags in treatment: 19522137 INFO @ Sun, 21 Jun 2020 18:15:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:15:12: #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 18:15:12: #1 tags after filtering in treatment: 19522074 INFO @ Sun, 21 Jun 2020 18:15:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:15:12: #1 finished! INFO @ Sun, 21 Jun 2020 18:15:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:15:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:15:13: #2 number of paired peaks: 391 WARNING @ Sun, 21 Jun 2020 18:15:13: Fewer paired peaks (391) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 391 pairs to build model! INFO @ Sun, 21 Jun 2020 18:15:13: start model_add_line... INFO @ Sun, 21 Jun 2020 18:15:13: start X-correlation... INFO @ Sun, 21 Jun 2020 18:15:13: end of X-cor INFO @ Sun, 21 Jun 2020 18:15:13: #2 finished! INFO @ Sun, 21 Jun 2020 18:15:13: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 18:15:13: #2 alternative fragment length(s) may be 3,56 bps INFO @ Sun, 21 Jun 2020 18:15:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.10_model.r WARNING @ Sun, 21 Jun 2020 18:15:13: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:15:13: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Sun, 21 Jun 2020 18:15:13: #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 18:15:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:15:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:15:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:15:17: 16000000 INFO @ Sun, 21 Jun 2020 18:15:23: 17000000 INFO @ Sun, 21 Jun 2020 18:15:29: 18000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:15:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:15:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:15:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.05_summits.bed INFO @ Sun, 21 Jun 2020 18:15:32: Done! pass1 - making usageList (586 chroms): 1 millis pass2 - checking and writing primary data (2943 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:15:35: 19000000 INFO @ Sun, 21 Jun 2020 18:15:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:15:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:15:39: #1 total tags in treatment: 19522137 INFO @ Sun, 21 Jun 2020 18:15:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:15:39: #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 18:15:39: #1 tags after filtering in treatment: 19522074 INFO @ Sun, 21 Jun 2020 18:15:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:15:39: #1 finished! INFO @ Sun, 21 Jun 2020 18:15:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:15:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:15:41: #2 number of paired peaks: 391 WARNING @ Sun, 21 Jun 2020 18:15:41: Fewer paired peaks (391) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 391 pairs to build model! INFO @ Sun, 21 Jun 2020 18:15:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:15:41: start X-correlation... INFO @ Sun, 21 Jun 2020 18:15:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:15:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:15:41: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 18:15:41: #2 alternative fragment length(s) may be 3,56 bps INFO @ Sun, 21 Jun 2020 18:15:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.20_model.r WARNING @ Sun, 21 Jun 2020 18:15:41: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:15:41: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Sun, 21 Jun 2020 18:15:41: #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 18:15:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:15:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:15:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:16:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:16:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:16:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.10_summits.bed INFO @ Sun, 21 Jun 2020 18:16:07: Done! pass1 - making usageList (358 chroms): 1 millis pass2 - checking and writing primary data (1299 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:16:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:16:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:16:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:16:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX159165/SRX159165.20_summits.bed INFO @ Sun, 21 Jun 2020 18:16:33: Done! pass1 - making usageList (229 chroms): 1 millis pass2 - checking and writing primary data (520 records, 4 fields): 9 millis CompletedMACS2peakCalling