Job ID = 6453869 SRX = SRX1537618 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:54:49 prefetch.2.10.7: 1) Downloading 'SRR3109313'... 2020-06-21T08:54:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:58:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:58:46 prefetch.2.10.7: 1) 'SRR3109313' was downloaded successfully Read 31326472 spots for SRR3109313/SRR3109313.sra Written 31326472 spots for SRR3109313/SRR3109313.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: 00:10:27 31326472 reads; of these: 31326472 (100.00%) were unpaired; of these: 1024359 (3.27%) aligned 0 times 21148142 (67.51%) aligned exactly 1 time 9153971 (29.22%) aligned >1 times 96.73% overall alignment rate Time searching: 00:10:28 Overall time: 00:10:28 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] 4778802 / 30302113 = 0.1577 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 18:18:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.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 18:18:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:18:25: 1000000 INFO @ Sun, 21 Jun 2020 18:18:30: 2000000 INFO @ Sun, 21 Jun 2020 18:18:35: 3000000 INFO @ Sun, 21 Jun 2020 18:18:40: 4000000 INFO @ Sun, 21 Jun 2020 18:18:45: 5000000 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 18:18:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.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 18:18:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:18:50: 6000000 INFO @ Sun, 21 Jun 2020 18:18:55: 1000000 INFO @ Sun, 21 Jun 2020 18:18:55: 7000000 INFO @ Sun, 21 Jun 2020 18:19:01: 2000000 INFO @ Sun, 21 Jun 2020 18:19:01: 8000000 INFO @ Sun, 21 Jun 2020 18:19:06: 3000000 INFO @ Sun, 21 Jun 2020 18:19:06: 9000000 INFO @ Sun, 21 Jun 2020 18:19:12: 4000000 INFO @ Sun, 21 Jun 2020 18:19:12: 10000000 INFO @ Sun, 21 Jun 2020 18:19:17: 5000000 INFO @ Sun, 21 Jun 2020 18:19:17: 11000000 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 18:19:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.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 18:19:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:22: 12000000 INFO @ Sun, 21 Jun 2020 18:19:23: 6000000 INFO @ Sun, 21 Jun 2020 18:19:25: 1000000 INFO @ Sun, 21 Jun 2020 18:19:28: 13000000 INFO @ Sun, 21 Jun 2020 18:19:28: 7000000 INFO @ Sun, 21 Jun 2020 18:19:31: 2000000 INFO @ Sun, 21 Jun 2020 18:19:33: 14000000 INFO @ Sun, 21 Jun 2020 18:19:34: 8000000 INFO @ Sun, 21 Jun 2020 18:19:36: 3000000 INFO @ Sun, 21 Jun 2020 18:19:38: 15000000 INFO @ Sun, 21 Jun 2020 18:19:39: 9000000 INFO @ Sun, 21 Jun 2020 18:19:41: 4000000 INFO @ Sun, 21 Jun 2020 18:19:44: 16000000 INFO @ Sun, 21 Jun 2020 18:19:45: 10000000 INFO @ Sun, 21 Jun 2020 18:19:46: 5000000 INFO @ Sun, 21 Jun 2020 18:19:49: 17000000 INFO @ Sun, 21 Jun 2020 18:19:50: 11000000 INFO @ Sun, 21 Jun 2020 18:19:52: 6000000 INFO @ Sun, 21 Jun 2020 18:19:54: 18000000 INFO @ Sun, 21 Jun 2020 18:19:56: 12000000 INFO @ Sun, 21 Jun 2020 18:19:57: 7000000 INFO @ Sun, 21 Jun 2020 18:19:59: 19000000 INFO @ Sun, 21 Jun 2020 18:20:01: 13000000 INFO @ Sun, 21 Jun 2020 18:20:02: 8000000 INFO @ Sun, 21 Jun 2020 18:20:05: 20000000 INFO @ Sun, 21 Jun 2020 18:20:07: 14000000 INFO @ Sun, 21 Jun 2020 18:20:08: 9000000 INFO @ Sun, 21 Jun 2020 18:20:10: 21000000 INFO @ Sun, 21 Jun 2020 18:20:12: 15000000 INFO @ Sun, 21 Jun 2020 18:20:13: 10000000 INFO @ Sun, 21 Jun 2020 18:20:15: 22000000 INFO @ Sun, 21 Jun 2020 18:20:17: 16000000 INFO @ Sun, 21 Jun 2020 18:20:18: 11000000 INFO @ Sun, 21 Jun 2020 18:20:21: 23000000 INFO @ Sun, 21 Jun 2020 18:20:23: 17000000 INFO @ Sun, 21 Jun 2020 18:20:24: 12000000 INFO @ Sun, 21 Jun 2020 18:20:26: 24000000 INFO @ Sun, 21 Jun 2020 18:20:28: 18000000 INFO @ Sun, 21 Jun 2020 18:20:29: 13000000 INFO @ Sun, 21 Jun 2020 18:20:31: 25000000 INFO @ Sun, 21 Jun 2020 18:20:34: 19000000 INFO @ Sun, 21 Jun 2020 18:20:34: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:20:34: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:20:34: #1 total tags in treatment: 25523311 INFO @ Sun, 21 Jun 2020 18:20:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:34: #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 18:20:34: 14000000 INFO @ Sun, 21 Jun 2020 18:20:35: #1 tags after filtering in treatment: 25523311 INFO @ Sun, 21 Jun 2020 18:20:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:36: #2 number of paired peaks: 482 WARNING @ Sun, 21 Jun 2020 18:20:36: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Sun, 21 Jun 2020 18:20:36: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:36: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:36: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:36: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:36: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:20:36: #2 alternative fragment length(s) may be 2 bps INFO @ Sun, 21 Jun 2020 18:20:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.05_model.r WARNING @ Sun, 21 Jun 2020 18:20:36: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:20:36: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sun, 21 Jun 2020 18:20:36: #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 18:20:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:39: 20000000 INFO @ Sun, 21 Jun 2020 18:20:40: 15000000 INFO @ Sun, 21 Jun 2020 18:20:45: 21000000 INFO @ Sun, 21 Jun 2020 18:20:45: 16000000 INFO @ Sun, 21 Jun 2020 18:20:50: 17000000 INFO @ Sun, 21 Jun 2020 18:20:50: 22000000 INFO @ Sun, 21 Jun 2020 18:20:55: 18000000 INFO @ Sun, 21 Jun 2020 18:20:56: 23000000 INFO @ Sun, 21 Jun 2020 18:21:01: 19000000 INFO @ Sun, 21 Jun 2020 18:21:01: 24000000 INFO @ Sun, 21 Jun 2020 18:21:06: 20000000 INFO @ Sun, 21 Jun 2020 18:21:06: 25000000 INFO @ Sun, 21 Jun 2020 18:21:09: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:21:09: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:21:09: #1 total tags in treatment: 25523311 INFO @ Sun, 21 Jun 2020 18:21:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:21:09: #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 18:21:10: #1 tags after filtering in treatment: 25523311 INFO @ Sun, 21 Jun 2020 18:21:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:21:10: #1 finished! INFO @ Sun, 21 Jun 2020 18:21:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:21:10: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:21:11: 21000000 INFO @ Sun, 21 Jun 2020 18:21:11: #2 number of paired peaks: 482 WARNING @ Sun, 21 Jun 2020 18:21:11: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Sun, 21 Jun 2020 18:21:11: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:12: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:12: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:12: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:12: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:21:12: #2 alternative fragment length(s) may be 2 bps INFO @ Sun, 21 Jun 2020 18:21:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.10_model.r WARNING @ Sun, 21 Jun 2020 18:21:12: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:21:12: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sun, 21 Jun 2020 18:21:12: #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 18:21:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:21:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:16: 22000000 INFO @ Sun, 21 Jun 2020 18:21:22: 23000000 INFO @ Sun, 21 Jun 2020 18:21:27: 24000000 INFO @ Sun, 21 Jun 2020 18:21:32: 25000000 INFO @ Sun, 21 Jun 2020 18:21:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.05_summits.bed INFO @ Sun, 21 Jun 2020 18:21:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:21:35: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:21:35: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:21:35: #1 total tags in treatment: 25523311 INFO @ Sun, 21 Jun 2020 18:21:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:21:35: #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 18:21:35: #1 tags after filtering in treatment: 25523311 INFO @ Sun, 21 Jun 2020 18:21:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:21:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:21:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:21:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:21:37: #2 number of paired peaks: 482 WARNING @ Sun, 21 Jun 2020 18:21:37: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Sun, 21 Jun 2020 18:21:37: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:37: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:37: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:37: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:37: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:21:37: #2 alternative fragment length(s) may be 2 bps INFO @ Sun, 21 Jun 2020 18:21:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.20_model.r WARNING @ Sun, 21 Jun 2020 18:21:37: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:21:37: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sun, 21 Jun 2020 18:21:37: #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 18:21:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:21:51: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:22:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:22:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:22:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.10_summits.bed INFO @ Sun, 21 Jun 2020 18:22:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:22:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:22:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:22:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:22:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1537618/SRX1537618.20_summits.bed INFO @ Sun, 21 Jun 2020 18:22:35: Done! pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling