Job ID = 6453161 SRX = SRX104976 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:04:54 prefetch.2.10.7: 1) Downloading 'SRR363420'... 2020-06-21T08:04:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:06:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:06:53 prefetch.2.10.7: 'SRR363420' is valid 2020-06-21T08:06:53 prefetch.2.10.7: 1) 'SRR363420' was downloaded successfully Read 21797397 spots for SRR363420/SRR363420.sra Written 21797397 spots for SRR363420/SRR363420.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: 00:04:46 21797397 reads; of these: 21797397 (100.00%) were unpaired; of these: 888526 (4.08%) aligned 0 times 16823482 (77.18%) aligned exactly 1 time 4085389 (18.74%) aligned >1 times 95.92% overall alignment rate Time searching: 00:04:46 Overall time: 00:04:46 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] 8497601 / 20908871 = 0.4064 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 17:16:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.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 17:16:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:16:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:16:21: 1000000 INFO @ Sun, 21 Jun 2020 17:16:27: 2000000 INFO @ Sun, 21 Jun 2020 17:16:34: 3000000 INFO @ Sun, 21 Jun 2020 17:16:40: 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 17:16:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.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 17:16:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:16:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:16:46: 5000000 INFO @ Sun, 21 Jun 2020 17:16:51: 1000000 INFO @ Sun, 21 Jun 2020 17:16:53: 6000000 INFO @ Sun, 21 Jun 2020 17:16:57: 2000000 INFO @ Sun, 21 Jun 2020 17:17:00: 7000000 INFO @ Sun, 21 Jun 2020 17:17:03: 3000000 INFO @ Sun, 21 Jun 2020 17:17:06: 8000000 INFO @ Sun, 21 Jun 2020 17:17:09: 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 17:17:13: 9000000 INFO @ Sun, 21 Jun 2020 17:17:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.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 17:17:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:17:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:17:16: 5000000 INFO @ Sun, 21 Jun 2020 17:17:20: 10000000 INFO @ Sun, 21 Jun 2020 17:17:21: 1000000 INFO @ Sun, 21 Jun 2020 17:17:22: 6000000 INFO @ Sun, 21 Jun 2020 17:17:27: 11000000 INFO @ Sun, 21 Jun 2020 17:17:27: 2000000 INFO @ Sun, 21 Jun 2020 17:17:28: 7000000 INFO @ Sun, 21 Jun 2020 17:17:34: 3000000 INFO @ Sun, 21 Jun 2020 17:17:34: 12000000 INFO @ Sun, 21 Jun 2020 17:17:34: 8000000 INFO @ Sun, 21 Jun 2020 17:17:37: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:17:37: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:17:37: #1 total tags in treatment: 12411270 INFO @ Sun, 21 Jun 2020 17:17:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:17:37: #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 17:17:38: #1 tags after filtering in treatment: 12411257 INFO @ Sun, 21 Jun 2020 17:17:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:17:38: #1 finished! INFO @ Sun, 21 Jun 2020 17:17:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:17:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:17:38: #2 number of paired peaks: 190 WARNING @ Sun, 21 Jun 2020 17:17:38: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Sun, 21 Jun 2020 17:17:38: start model_add_line... INFO @ Sun, 21 Jun 2020 17:17:38: start X-correlation... INFO @ Sun, 21 Jun 2020 17:17:38: end of X-cor INFO @ Sun, 21 Jun 2020 17:17:38: #2 finished! INFO @ Sun, 21 Jun 2020 17:17:38: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 17:17:38: #2 alternative fragment length(s) may be 52 bps INFO @ Sun, 21 Jun 2020 17:17:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.05_model.r WARNING @ Sun, 21 Jun 2020 17:17:38: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:17:38: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sun, 21 Jun 2020 17:17:38: #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 17:17:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:17:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:17:40: 4000000 INFO @ Sun, 21 Jun 2020 17:17:40: 9000000 INFO @ Sun, 21 Jun 2020 17:17:46: 5000000 INFO @ Sun, 21 Jun 2020 17:17:46: 10000000 INFO @ Sun, 21 Jun 2020 17:17:52: 6000000 INFO @ Sun, 21 Jun 2020 17:17:52: 11000000 INFO @ Sun, 21 Jun 2020 17:17:57: 7000000 INFO @ Sun, 21 Jun 2020 17:17:58: 12000000 INFO @ Sun, 21 Jun 2020 17:18:01: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:18:01: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:18:01: #1 total tags in treatment: 12411270 INFO @ Sun, 21 Jun 2020 17:18:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:18:01: #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 17:18:01: #1 tags after filtering in treatment: 12411257 INFO @ Sun, 21 Jun 2020 17:18:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:18:01: #1 finished! INFO @ Sun, 21 Jun 2020 17:18:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:18:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:18:02: #2 number of paired peaks: 190 WARNING @ Sun, 21 Jun 2020 17:18:02: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Sun, 21 Jun 2020 17:18:02: start model_add_line... INFO @ Sun, 21 Jun 2020 17:18:02: start X-correlation... INFO @ Sun, 21 Jun 2020 17:18:02: end of X-cor INFO @ Sun, 21 Jun 2020 17:18:02: #2 finished! INFO @ Sun, 21 Jun 2020 17:18:02: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 17:18:02: #2 alternative fragment length(s) may be 52 bps INFO @ Sun, 21 Jun 2020 17:18:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.10_model.r WARNING @ Sun, 21 Jun 2020 17:18:02: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:18:02: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sun, 21 Jun 2020 17:18:02: #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 17:18:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:18:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:18:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:18:03: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:18:09: 9000000 INFO @ Sun, 21 Jun 2020 17:18:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:18:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:18:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.05_summits.bed INFO @ Sun, 21 Jun 2020 17:18:15: Done! INFO @ Sun, 21 Jun 2020 17:18:15: 10000000 pass1 - making usageList (287 chroms): 1 millis pass2 - checking and writing primary data (877 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:18:20: 11000000 INFO @ Sun, 21 Jun 2020 17:18:25: 12000000 INFO @ Sun, 21 Jun 2020 17:18:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:18:28: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:18:28: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:18:28: #1 total tags in treatment: 12411270 INFO @ Sun, 21 Jun 2020 17:18:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:18:28: #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 17:18:28: #1 tags after filtering in treatment: 12411257 INFO @ Sun, 21 Jun 2020 17:18:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:18:28: #1 finished! INFO @ Sun, 21 Jun 2020 17:18:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:18:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:18:29: #2 number of paired peaks: 190 WARNING @ Sun, 21 Jun 2020 17:18:29: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Sun, 21 Jun 2020 17:18:29: start model_add_line... INFO @ Sun, 21 Jun 2020 17:18:29: start X-correlation... INFO @ Sun, 21 Jun 2020 17:18:29: end of X-cor INFO @ Sun, 21 Jun 2020 17:18:29: #2 finished! INFO @ Sun, 21 Jun 2020 17:18:29: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 17:18:29: #2 alternative fragment length(s) may be 52 bps INFO @ Sun, 21 Jun 2020 17:18:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.20_model.r WARNING @ Sun, 21 Jun 2020 17:18:29: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:18:29: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sun, 21 Jun 2020 17:18:29: #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 17:18:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:18:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:18:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:18:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:18:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.10_summits.bed INFO @ Sun, 21 Jun 2020 17:18:38: Done! pass1 - making usageList (161 chroms): 1 millis pass2 - checking and writing primary data (392 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:18:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:19:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:19:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:19:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104976/SRX104976.20_summits.bed INFO @ Sun, 21 Jun 2020 17:19:05: Done! pass1 - making usageList (88 chroms): 1 millis pass2 - checking and writing primary data (165 records, 4 fields): 4 millis CompletedMACS2peakCalling