Job ID = 6452904 SRX = SRX042247 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:56:30 prefetch.2.10.7: 1) Downloading 'SRR100228'... 2020-06-21T07:56:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:05:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:05:57 prefetch.2.10.7: 1) 'SRR100228' was downloaded successfully Read 34089738 spots for SRR100228/SRR100228.sra Written 34089738 spots for SRR100228/SRR100228.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: 00:10:40 34089738 reads; of these: 34089738 (100.00%) were unpaired; of these: 4377954 (12.84%) aligned 0 times 27936579 (81.95%) aligned exactly 1 time 1775205 (5.21%) aligned >1 times 87.16% overall alignment rate Time searching: 00:10:40 Overall time: 00:10:40 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] 13226516 / 29711784 = 0.4452 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 17:26:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.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 17:26:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:26:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:27:00: 1000000 INFO @ Sun, 21 Jun 2020 17:27:08: 2000000 INFO @ Sun, 21 Jun 2020 17:27:15: 3000000 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 17:27:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.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 17:27:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:27:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:27:23: 4000000 INFO @ Sun, 21 Jun 2020 17:27:29: 1000000 INFO @ Sun, 21 Jun 2020 17:27:31: 5000000 INFO @ Sun, 21 Jun 2020 17:27:37: 2000000 INFO @ Sun, 21 Jun 2020 17:27:39: 6000000 INFO @ Sun, 21 Jun 2020 17:27:44: 3000000 INFO @ Sun, 21 Jun 2020 17:27:48: 7000000 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 17:27:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.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 17:27:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:27:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:27:53: 4000000 INFO @ Sun, 21 Jun 2020 17:27:56: 8000000 INFO @ Sun, 21 Jun 2020 17:28:00: 1000000 INFO @ Sun, 21 Jun 2020 17:28:01: 5000000 INFO @ Sun, 21 Jun 2020 17:28:04: 9000000 INFO @ Sun, 21 Jun 2020 17:28:07: 2000000 INFO @ Sun, 21 Jun 2020 17:28:08: 6000000 INFO @ Sun, 21 Jun 2020 17:28:13: 10000000 INFO @ Sun, 21 Jun 2020 17:28:15: 3000000 INFO @ Sun, 21 Jun 2020 17:28:16: 7000000 INFO @ Sun, 21 Jun 2020 17:28:21: 11000000 INFO @ Sun, 21 Jun 2020 17:28:22: 4000000 INFO @ Sun, 21 Jun 2020 17:28:23: 8000000 INFO @ Sun, 21 Jun 2020 17:28:30: 12000000 INFO @ Sun, 21 Jun 2020 17:28:30: 5000000 INFO @ Sun, 21 Jun 2020 17:28:31: 9000000 INFO @ Sun, 21 Jun 2020 17:28:37: 6000000 INFO @ Sun, 21 Jun 2020 17:28:38: 13000000 INFO @ Sun, 21 Jun 2020 17:28:40: 10000000 INFO @ Sun, 21 Jun 2020 17:28:45: 7000000 INFO @ Sun, 21 Jun 2020 17:28:47: 14000000 INFO @ Sun, 21 Jun 2020 17:28:48: 11000000 INFO @ Sun, 21 Jun 2020 17:28:52: 8000000 INFO @ Sun, 21 Jun 2020 17:28:55: 15000000 INFO @ Sun, 21 Jun 2020 17:28:56: 12000000 INFO @ Sun, 21 Jun 2020 17:28:59: 9000000 INFO @ Sun, 21 Jun 2020 17:29:03: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:29:05: 13000000 INFO @ Sun, 21 Jun 2020 17:29:06: 10000000 INFO @ Sun, 21 Jun 2020 17:29:08: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:29:08: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:29:08: #1 total tags in treatment: 16485268 INFO @ Sun, 21 Jun 2020 17:29:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:29:08: #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 17:29:08: #1 tags after filtering in treatment: 16484917 INFO @ Sun, 21 Jun 2020 17:29:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:29:08: #1 finished! INFO @ Sun, 21 Jun 2020 17:29:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:29:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:29:10: #2 number of paired peaks: 2994 INFO @ Sun, 21 Jun 2020 17:29:10: start model_add_line... INFO @ Sun, 21 Jun 2020 17:29:10: start X-correlation... INFO @ Sun, 21 Jun 2020 17:29:10: end of X-cor INFO @ Sun, 21 Jun 2020 17:29:10: #2 finished! INFO @ Sun, 21 Jun 2020 17:29:10: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 17:29:10: #2 alternative fragment length(s) may be 1 bps INFO @ Sun, 21 Jun 2020 17:29:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.05_model.r WARNING @ Sun, 21 Jun 2020 17:29:10: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:29:10: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sun, 21 Jun 2020 17:29:10: #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 17:29:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:29:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:29:13: 14000000 INFO @ Sun, 21 Jun 2020 17:29:13: 11000000 INFO @ Sun, 21 Jun 2020 17:29:21: 12000000 INFO @ Sun, 21 Jun 2020 17:29:21: 15000000 INFO @ Sun, 21 Jun 2020 17:29:28: 13000000 INFO @ Sun, 21 Jun 2020 17:29:29: 16000000 INFO @ Sun, 21 Jun 2020 17:29:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:29:33: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:29:33: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:29:33: #1 total tags in treatment: 16485268 INFO @ Sun, 21 Jun 2020 17:29:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:29:33: #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 17:29:34: #1 tags after filtering in treatment: 16484917 INFO @ Sun, 21 Jun 2020 17:29:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:29:34: #1 finished! INFO @ Sun, 21 Jun 2020 17:29:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:29:34: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:29:35: 14000000 INFO @ Sun, 21 Jun 2020 17:29:35: #2 number of paired peaks: 2994 INFO @ Sun, 21 Jun 2020 17:29:35: start model_add_line... INFO @ Sun, 21 Jun 2020 17:29:35: start X-correlation... INFO @ Sun, 21 Jun 2020 17:29:35: end of X-cor INFO @ Sun, 21 Jun 2020 17:29:35: #2 finished! INFO @ Sun, 21 Jun 2020 17:29:35: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 17:29:35: #2 alternative fragment length(s) may be 1 bps INFO @ Sun, 21 Jun 2020 17:29:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.10_model.r WARNING @ Sun, 21 Jun 2020 17:29:35: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:29:35: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sun, 21 Jun 2020 17:29:35: #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 17:29:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:29:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:29:42: 15000000 INFO @ Sun, 21 Jun 2020 17:29:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:29:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:29:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.05_summits.bed INFO @ Sun, 21 Jun 2020 17:29:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:29:48: 16000000 INFO @ Sun, 21 Jun 2020 17:29:51: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:29:51: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:29:51: #1 total tags in treatment: 16485268 INFO @ Sun, 21 Jun 2020 17:29:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:29:51: #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 17:29:52: #1 tags after filtering in treatment: 16484917 INFO @ Sun, 21 Jun 2020 17:29:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:29:52: #1 finished! INFO @ Sun, 21 Jun 2020 17:29:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:29:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:29:53: #2 number of paired peaks: 2994 INFO @ Sun, 21 Jun 2020 17:29:53: start model_add_line... INFO @ Sun, 21 Jun 2020 17:29:53: start X-correlation... INFO @ Sun, 21 Jun 2020 17:29:53: end of X-cor INFO @ Sun, 21 Jun 2020 17:29:53: #2 finished! INFO @ Sun, 21 Jun 2020 17:29:53: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 17:29:53: #2 alternative fragment length(s) may be 1 bps INFO @ Sun, 21 Jun 2020 17:29:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.20_model.r WARNING @ Sun, 21 Jun 2020 17:29:53: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:29:53: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sun, 21 Jun 2020 17:29:53: #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 17:29:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:29:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:29:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:30:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:30:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:30:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.10_summits.bed INFO @ Sun, 21 Jun 2020 17:30:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:30:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:30:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:30:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:30:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX042247/SRX042247.20_summits.bed INFO @ Sun, 21 Jun 2020 17:30:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling