Job ID = 6454032 SRX = SRX1794218 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:45:17 prefetch.2.10.7: 1) Downloading 'SRR3575250'... 2020-06-21T08:45:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:50:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:50:52 prefetch.2.10.7: 'SRR3575250' is valid 2020-06-21T08:50:52 prefetch.2.10.7: 1) 'SRR3575250' was downloaded successfully 2020-06-21T08:50:52 prefetch.2.10.7: 'SRR3575250' has 0 unresolved dependencies Read 26251872 spots for SRR3575250/SRR3575250.sra Written 26251872 spots for SRR3575250/SRR3575250.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: 00:05:56 26251872 reads; of these: 26251872 (100.00%) were unpaired; of these: 7620284 (29.03%) aligned 0 times 13121701 (49.98%) aligned exactly 1 time 5509887 (20.99%) aligned >1 times 70.97% overall alignment rate Time searching: 00:05:56 Overall time: 00:05:56 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 8 files... [bam_rmdupse_core] 2582376 / 18631588 = 0.1386 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 18:02:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.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 18:02:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:02:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:02:25: 1000000 INFO @ Sun, 21 Jun 2020 18:02:31: 2000000 INFO @ Sun, 21 Jun 2020 18:02:36: 3000000 INFO @ Sun, 21 Jun 2020 18:02:42: 4000000 INFO @ Sun, 21 Jun 2020 18:02:47: 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 18:02:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.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 18:02:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:02:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:02:53: 6000000 INFO @ Sun, 21 Jun 2020 18:02:55: 1000000 INFO @ Sun, 21 Jun 2020 18:02:58: 7000000 INFO @ Sun, 21 Jun 2020 18:03:01: 2000000 INFO @ Sun, 21 Jun 2020 18:03:04: 8000000 INFO @ Sun, 21 Jun 2020 18:03:06: 3000000 INFO @ Sun, 21 Jun 2020 18:03:09: 9000000 INFO @ Sun, 21 Jun 2020 18:03:12: 4000000 INFO @ Sun, 21 Jun 2020 18:03:15: 10000000 INFO @ Sun, 21 Jun 2020 18:03:17: 5000000 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 18:03:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.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 18:03:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:03:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:03:20: 11000000 INFO @ Sun, 21 Jun 2020 18:03:23: 6000000 INFO @ Sun, 21 Jun 2020 18:03:25: 1000000 INFO @ Sun, 21 Jun 2020 18:03:26: 12000000 INFO @ Sun, 21 Jun 2020 18:03:28: 7000000 INFO @ Sun, 21 Jun 2020 18:03:31: 2000000 INFO @ Sun, 21 Jun 2020 18:03:31: 13000000 INFO @ Sun, 21 Jun 2020 18:03:34: 8000000 INFO @ Sun, 21 Jun 2020 18:03:37: 14000000 INFO @ Sun, 21 Jun 2020 18:03:37: 3000000 INFO @ Sun, 21 Jun 2020 18:03:40: 9000000 INFO @ Sun, 21 Jun 2020 18:03:42: 15000000 INFO @ Sun, 21 Jun 2020 18:03:43: 4000000 INFO @ Sun, 21 Jun 2020 18:03:45: 10000000 INFO @ Sun, 21 Jun 2020 18:03:48: 16000000 INFO @ Sun, 21 Jun 2020 18:03:48: 5000000 INFO @ Sun, 21 Jun 2020 18:03:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:03:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:03:49: #1 total tags in treatment: 16049212 INFO @ Sun, 21 Jun 2020 18:03:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:03:49: #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 18:03:49: #1 tags after filtering in treatment: 16049144 INFO @ Sun, 21 Jun 2020 18:03:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:03:49: #1 finished! INFO @ Sun, 21 Jun 2020 18:03:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:03:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:03:50: #2 number of paired peaks: 628 WARNING @ Sun, 21 Jun 2020 18:03:50: Fewer paired peaks (628) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 628 pairs to build model! INFO @ Sun, 21 Jun 2020 18:03:50: start model_add_line... INFO @ Sun, 21 Jun 2020 18:03:51: start X-correlation... INFO @ Sun, 21 Jun 2020 18:03:51: end of X-cor INFO @ Sun, 21 Jun 2020 18:03:51: #2 finished! INFO @ Sun, 21 Jun 2020 18:03:51: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 18:03:51: #2 alternative fragment length(s) may be 2,47,583 bps INFO @ Sun, 21 Jun 2020 18:03:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.05_model.r WARNING @ Sun, 21 Jun 2020 18:03:51: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:03:51: #2 You may need to consider one of the other alternative d(s): 2,47,583 WARNING @ Sun, 21 Jun 2020 18:03:51: #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 18:03:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:03:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:03:51: 11000000 INFO @ Sun, 21 Jun 2020 18:03:54: 6000000 INFO @ Sun, 21 Jun 2020 18:03:56: 12000000 INFO @ Sun, 21 Jun 2020 18:04:00: 7000000 INFO @ Sun, 21 Jun 2020 18:04:02: 13000000 INFO @ Sun, 21 Jun 2020 18:04:06: 8000000 INFO @ Sun, 21 Jun 2020 18:04:07: 14000000 INFO @ Sun, 21 Jun 2020 18:04:11: 9000000 INFO @ Sun, 21 Jun 2020 18:04:13: 15000000 INFO @ Sun, 21 Jun 2020 18:04:17: 10000000 INFO @ Sun, 21 Jun 2020 18:04:18: 16000000 INFO @ Sun, 21 Jun 2020 18:04:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:04:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:04:19: #1 total tags in treatment: 16049212 INFO @ Sun, 21 Jun 2020 18:04:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:04:19: #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 18:04:19: #1 tags after filtering in treatment: 16049144 INFO @ Sun, 21 Jun 2020 18:04:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:04:19: #1 finished! INFO @ Sun, 21 Jun 2020 18:04:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:04:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:04:20: #2 number of paired peaks: 628 WARNING @ Sun, 21 Jun 2020 18:04:20: Fewer paired peaks (628) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 628 pairs to build model! INFO @ Sun, 21 Jun 2020 18:04:20: start model_add_line... INFO @ Sun, 21 Jun 2020 18:04:21: start X-correlation... INFO @ Sun, 21 Jun 2020 18:04:21: end of X-cor INFO @ Sun, 21 Jun 2020 18:04:21: #2 finished! INFO @ Sun, 21 Jun 2020 18:04:21: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 18:04:21: #2 alternative fragment length(s) may be 2,47,583 bps INFO @ Sun, 21 Jun 2020 18:04:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.10_model.r WARNING @ Sun, 21 Jun 2020 18:04:21: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:04:21: #2 You may need to consider one of the other alternative d(s): 2,47,583 WARNING @ Sun, 21 Jun 2020 18:04:21: #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 18:04:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:04:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:04:22: 11000000 INFO @ Sun, 21 Jun 2020 18:04:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:04:28: 12000000 INFO @ Sun, 21 Jun 2020 18:04:33: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:04:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:04:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:04:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.05_summits.bed INFO @ Sun, 21 Jun 2020 18:04:38: Done! pass1 - making usageList (637 chroms): 1 millis pass2 - checking and writing primary data (2839 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:04:39: 14000000 INFO @ Sun, 21 Jun 2020 18:04:44: 15000000 INFO @ Sun, 21 Jun 2020 18:04:50: 16000000 INFO @ Sun, 21 Jun 2020 18:04:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:04:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:04:50: #1 total tags in treatment: 16049212 INFO @ Sun, 21 Jun 2020 18:04:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:04:50: #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 18:04:51: #1 tags after filtering in treatment: 16049144 INFO @ Sun, 21 Jun 2020 18:04:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:04:51: #1 finished! INFO @ Sun, 21 Jun 2020 18:04:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:04:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:04:52: #2 number of paired peaks: 628 WARNING @ Sun, 21 Jun 2020 18:04:52: Fewer paired peaks (628) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 628 pairs to build model! INFO @ Sun, 21 Jun 2020 18:04:52: start model_add_line... INFO @ Sun, 21 Jun 2020 18:04:52: start X-correlation... INFO @ Sun, 21 Jun 2020 18:04:52: end of X-cor INFO @ Sun, 21 Jun 2020 18:04:52: #2 finished! INFO @ Sun, 21 Jun 2020 18:04:52: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 18:04:52: #2 alternative fragment length(s) may be 2,47,583 bps INFO @ Sun, 21 Jun 2020 18:04:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.20_model.r WARNING @ Sun, 21 Jun 2020 18:04:52: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:04:52: #2 You may need to consider one of the other alternative d(s): 2,47,583 WARNING @ Sun, 21 Jun 2020 18:04:52: #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 18:04:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:04:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:04:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:05:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:05:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:05:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.10_summits.bed INFO @ Sun, 21 Jun 2020 18:05:07: Done! BigWig に変換しました。 pass1 - making usageList (437 chroms): 1 millis pass2 - checking and writing primary data (1303 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:05:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:05:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:05:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:05:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794218/SRX1794218.20_summits.bed INFO @ Sun, 21 Jun 2020 18:05:38: Done! pass1 - making usageList (186 chroms): 1 millis pass2 - checking and writing primary data (416 records, 4 fields): 6 millis CompletedMACS2peakCalling