Job ID = 6527809 SRX = SRX287709 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:19:49 prefetch.2.10.7: 1) Downloading 'SRR869897'... 2020-06-29T13:19:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:22:45 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:22:45 prefetch.2.10.7: 1) 'SRR869897' was downloaded successfully Read 22382823 spots for SRR869897/SRR869897.sra Written 22382823 spots for SRR869897/SRR869897.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: 00:07:58 22382823 reads; of these: 22382823 (100.00%) were unpaired; of these: 1147784 (5.13%) aligned 0 times 14422397 (64.44%) aligned exactly 1 time 6812642 (30.44%) aligned >1 times 94.87% overall alignment rate Time searching: 00:07:58 Overall time: 00:07:58 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4906147 / 21235039 = 0.2310 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 @ Mon, 29 Jun 2020 22:45:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.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 @ Mon, 29 Jun 2020 22:45:22: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:45:22: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:45:28: 1000000 INFO @ Mon, 29 Jun 2020 22:45:34: 2000000 INFO @ Mon, 29 Jun 2020 22:45:40: 3000000 INFO @ Mon, 29 Jun 2020 22:45:46: 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 @ Mon, 29 Jun 2020 22:45:51: 5000000 INFO @ Mon, 29 Jun 2020 22:45:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.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 @ Mon, 29 Jun 2020 22:45:52: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:45:52: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:45:57: 6000000 INFO @ Mon, 29 Jun 2020 22:45:58: 1000000 INFO @ Mon, 29 Jun 2020 22:46:03: 7000000 INFO @ Mon, 29 Jun 2020 22:46:04: 2000000 INFO @ Mon, 29 Jun 2020 22:46:09: 8000000 INFO @ Mon, 29 Jun 2020 22:46:10: 3000000 INFO @ Mon, 29 Jun 2020 22:46:15: 9000000 INFO @ Mon, 29 Jun 2020 22:46:16: 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 @ Mon, 29 Jun 2020 22:46:21: 10000000 INFO @ Mon, 29 Jun 2020 22:46:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.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 @ Mon, 29 Jun 2020 22:46:22: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:46:22: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:46:23: 5000000 INFO @ Mon, 29 Jun 2020 22:46:27: 11000000 INFO @ Mon, 29 Jun 2020 22:46:29: 1000000 INFO @ Mon, 29 Jun 2020 22:46:29: 6000000 INFO @ Mon, 29 Jun 2020 22:46:32: 12000000 INFO @ Mon, 29 Jun 2020 22:46:35: 2000000 INFO @ Mon, 29 Jun 2020 22:46:36: 7000000 INFO @ Mon, 29 Jun 2020 22:46:38: 13000000 INFO @ Mon, 29 Jun 2020 22:46:41: 3000000 INFO @ Mon, 29 Jun 2020 22:46:42: 8000000 INFO @ Mon, 29 Jun 2020 22:46:44: 14000000 INFO @ Mon, 29 Jun 2020 22:46:48: 4000000 INFO @ Mon, 29 Jun 2020 22:46:48: 9000000 INFO @ Mon, 29 Jun 2020 22:46:50: 15000000 INFO @ Mon, 29 Jun 2020 22:46:54: 5000000 INFO @ Mon, 29 Jun 2020 22:46:54: 10000000 INFO @ Mon, 29 Jun 2020 22:46:56: 16000000 INFO @ Mon, 29 Jun 2020 22:46:58: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:46:58: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:46:58: #1 total tags in treatment: 16328892 INFO @ Mon, 29 Jun 2020 22:46:58: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:46:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:46:58: #1 tags after filtering in treatment: 16328892 INFO @ Mon, 29 Jun 2020 22:46:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:46:58: #1 finished! INFO @ Mon, 29 Jun 2020 22:46:58: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:46:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:47:00: #2 number of paired peaks: 191 WARNING @ Mon, 29 Jun 2020 22:47:00: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Mon, 29 Jun 2020 22:47:00: start model_add_line... INFO @ Mon, 29 Jun 2020 22:47:00: start X-correlation... INFO @ Mon, 29 Jun 2020 22:47:00: end of X-cor INFO @ Mon, 29 Jun 2020 22:47:00: #2 finished! INFO @ Mon, 29 Jun 2020 22:47:00: #2 predicted fragment length is 44 bps INFO @ Mon, 29 Jun 2020 22:47:00: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 29 Jun 2020 22:47:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.05_model.r WARNING @ Mon, 29 Jun 2020 22:47:00: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:47:00: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 29 Jun 2020 22:47:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:47:00: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:47:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:47:00: 6000000 INFO @ Mon, 29 Jun 2020 22:47:01: 11000000 INFO @ Mon, 29 Jun 2020 22:47:07: 7000000 INFO @ Mon, 29 Jun 2020 22:47:07: 12000000 INFO @ Mon, 29 Jun 2020 22:47:13: 8000000 INFO @ Mon, 29 Jun 2020 22:47:13: 13000000 INFO @ Mon, 29 Jun 2020 22:47:19: 9000000 INFO @ Mon, 29 Jun 2020 22:47:20: 14000000 INFO @ Mon, 29 Jun 2020 22:47:25: 10000000 INFO @ Mon, 29 Jun 2020 22:47:26: 15000000 INFO @ Mon, 29 Jun 2020 22:47:27: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:47:32: 11000000 INFO @ Mon, 29 Jun 2020 22:47:32: 16000000 INFO @ Mon, 29 Jun 2020 22:47:35: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:47:35: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:47:35: #1 total tags in treatment: 16328892 INFO @ Mon, 29 Jun 2020 22:47:35: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:47:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:47:35: #1 tags after filtering in treatment: 16328892 INFO @ Mon, 29 Jun 2020 22:47:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:47:35: #1 finished! INFO @ Mon, 29 Jun 2020 22:47:35: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:47:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:47:36: #2 number of paired peaks: 191 WARNING @ Mon, 29 Jun 2020 22:47:36: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Mon, 29 Jun 2020 22:47:36: start model_add_line... INFO @ Mon, 29 Jun 2020 22:47:36: start X-correlation... INFO @ Mon, 29 Jun 2020 22:47:36: end of X-cor INFO @ Mon, 29 Jun 2020 22:47:36: #2 finished! INFO @ Mon, 29 Jun 2020 22:47:36: #2 predicted fragment length is 44 bps INFO @ Mon, 29 Jun 2020 22:47:36: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 29 Jun 2020 22:47:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.10_model.r WARNING @ Mon, 29 Jun 2020 22:47:36: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:47:36: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 29 Jun 2020 22:47:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:47:36: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:47:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:47:38: 12000000 INFO @ Mon, 29 Jun 2020 22:47:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:47:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:47:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.05_summits.bed INFO @ Mon, 29 Jun 2020 22:47:42: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2184 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:47:45: 13000000 INFO @ Mon, 29 Jun 2020 22:47:52: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:47:58: 15000000 INFO @ Mon, 29 Jun 2020 22:48:03: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:48:04: 16000000 INFO @ Mon, 29 Jun 2020 22:48:06: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:48:06: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:48:06: #1 total tags in treatment: 16328892 INFO @ Mon, 29 Jun 2020 22:48:06: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:48:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:48:06: #1 tags after filtering in treatment: 16328892 INFO @ Mon, 29 Jun 2020 22:48:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:48:06: #1 finished! INFO @ Mon, 29 Jun 2020 22:48:06: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:48:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:48:07: #2 number of paired peaks: 191 WARNING @ Mon, 29 Jun 2020 22:48:07: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Mon, 29 Jun 2020 22:48:07: start model_add_line... INFO @ Mon, 29 Jun 2020 22:48:07: start X-correlation... INFO @ Mon, 29 Jun 2020 22:48:07: end of X-cor INFO @ Mon, 29 Jun 2020 22:48:07: #2 finished! INFO @ Mon, 29 Jun 2020 22:48:07: #2 predicted fragment length is 44 bps INFO @ Mon, 29 Jun 2020 22:48:07: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 29 Jun 2020 22:48:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.20_model.r WARNING @ Mon, 29 Jun 2020 22:48:07: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:48:07: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 29 Jun 2020 22:48:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:48:07: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:48:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:48:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:48:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:48:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.10_summits.bed INFO @ Mon, 29 Jun 2020 22:48:18: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1813 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:48:35: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:48:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:48:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:48:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287709/SRX287709.20_summits.bed INFO @ Mon, 29 Jun 2020 22:48:50: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1292 records, 4 fields): 4 millis CompletedMACS2peakCalling