Job ID = 6457568 SRX = SRX4669052 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:59:03 prefetch.2.10.7: 1) Downloading 'SRR7817577'... 2020-06-21T11:59:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:00:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:00:45 prefetch.2.10.7: 'SRR7817577' is valid 2020-06-21T12:00:45 prefetch.2.10.7: 1) 'SRR7817577' was downloaded successfully 2020-06-21T12:00:45 prefetch.2.10.7: 'SRR7817577' has 0 unresolved dependencies Read 29694717 spots for SRR7817577/SRR7817577.sra Written 29694717 spots for SRR7817577/SRR7817577.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: 00:05:53 29694717 reads; of these: 29694717 (100.00%) were unpaired; of these: 4279286 (14.41%) aligned 0 times 22917979 (77.18%) aligned exactly 1 time 2497452 (8.41%) aligned >1 times 85.59% overall alignment rate Time searching: 00:05:53 Overall time: 00:05:53 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 12 files... [bam_rmdupse_core] 6813172 / 25415431 = 0.2681 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 21:14:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.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 21:14:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:14:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:14:09: 1000000 INFO @ Sun, 21 Jun 2020 21:14:15: 2000000 INFO @ Sun, 21 Jun 2020 21:14:21: 3000000 INFO @ Sun, 21 Jun 2020 21:14:27: 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 21:14:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.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 21:14:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:14:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:14:34: 5000000 INFO @ Sun, 21 Jun 2020 21:14:40: 1000000 INFO @ Sun, 21 Jun 2020 21:14:41: 6000000 INFO @ Sun, 21 Jun 2020 21:14:47: 2000000 INFO @ Sun, 21 Jun 2020 21:14:48: 7000000 INFO @ Sun, 21 Jun 2020 21:14:54: 3000000 INFO @ Sun, 21 Jun 2020 21:14:55: 8000000 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 21:15:01: 4000000 INFO @ Sun, 21 Jun 2020 21:15:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.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 21:15:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:15:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:15:02: 9000000 INFO @ Sun, 21 Jun 2020 21:15:09: 5000000 INFO @ Sun, 21 Jun 2020 21:15:10: 10000000 INFO @ Sun, 21 Jun 2020 21:15:10: 1000000 INFO @ Sun, 21 Jun 2020 21:15:17: 6000000 INFO @ Sun, 21 Jun 2020 21:15:17: 11000000 INFO @ Sun, 21 Jun 2020 21:15:18: 2000000 INFO @ Sun, 21 Jun 2020 21:15:25: 12000000 INFO @ Sun, 21 Jun 2020 21:15:25: 7000000 INFO @ Sun, 21 Jun 2020 21:15:26: 3000000 INFO @ Sun, 21 Jun 2020 21:15:32: 13000000 INFO @ Sun, 21 Jun 2020 21:15:32: 8000000 INFO @ Sun, 21 Jun 2020 21:15:34: 4000000 INFO @ Sun, 21 Jun 2020 21:15:40: 14000000 INFO @ Sun, 21 Jun 2020 21:15:40: 9000000 INFO @ Sun, 21 Jun 2020 21:15:42: 5000000 INFO @ Sun, 21 Jun 2020 21:15:47: 10000000 INFO @ Sun, 21 Jun 2020 21:15:47: 15000000 INFO @ Sun, 21 Jun 2020 21:15:50: 6000000 INFO @ Sun, 21 Jun 2020 21:15:55: 11000000 INFO @ Sun, 21 Jun 2020 21:15:56: 16000000 INFO @ Sun, 21 Jun 2020 21:15:58: 7000000 INFO @ Sun, 21 Jun 2020 21:16:02: 12000000 INFO @ Sun, 21 Jun 2020 21:16:04: 17000000 INFO @ Sun, 21 Jun 2020 21:16:06: 8000000 INFO @ Sun, 21 Jun 2020 21:16:10: 13000000 INFO @ Sun, 21 Jun 2020 21:16:12: 18000000 INFO @ Sun, 21 Jun 2020 21:16:13: 9000000 INFO @ Sun, 21 Jun 2020 21:16:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:16:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:16:17: #1 total tags in treatment: 18602259 INFO @ Sun, 21 Jun 2020 21:16:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:16:17: #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 21:16:17: 14000000 INFO @ Sun, 21 Jun 2020 21:16:18: #1 tags after filtering in treatment: 18602227 INFO @ Sun, 21 Jun 2020 21:16:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:16:18: #1 finished! INFO @ Sun, 21 Jun 2020 21:16:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:16:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:16:19: #2 number of paired peaks: 168 WARNING @ Sun, 21 Jun 2020 21:16:19: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Sun, 21 Jun 2020 21:16:19: start model_add_line... INFO @ Sun, 21 Jun 2020 21:16:19: start X-correlation... INFO @ Sun, 21 Jun 2020 21:16:19: end of X-cor INFO @ Sun, 21 Jun 2020 21:16:19: #2 finished! INFO @ Sun, 21 Jun 2020 21:16:19: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 21:16:19: #2 alternative fragment length(s) may be 3,63,541,572 bps INFO @ Sun, 21 Jun 2020 21:16:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.05_model.r WARNING @ Sun, 21 Jun 2020 21:16:19: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:16:19: #2 You may need to consider one of the other alternative d(s): 3,63,541,572 WARNING @ Sun, 21 Jun 2020 21:16:19: #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 21:16:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:16:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:16:21: 10000000 INFO @ Sun, 21 Jun 2020 21:16:25: 15000000 INFO @ Sun, 21 Jun 2020 21:16:28: 11000000 INFO @ Sun, 21 Jun 2020 21:16:33: 16000000 INFO @ Sun, 21 Jun 2020 21:16:35: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:16:41: 17000000 INFO @ Sun, 21 Jun 2020 21:16:42: 13000000 INFO @ Sun, 21 Jun 2020 21:16:48: 18000000 INFO @ Sun, 21 Jun 2020 21:16:50: 14000000 INFO @ Sun, 21 Jun 2020 21:16:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:16:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:16:53: #1 total tags in treatment: 18602259 INFO @ Sun, 21 Jun 2020 21:16:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:16:53: #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 21:16:54: #1 tags after filtering in treatment: 18602227 INFO @ Sun, 21 Jun 2020 21:16:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:16:54: #1 finished! INFO @ Sun, 21 Jun 2020 21:16:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:16:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:16:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:16:55: #2 number of paired peaks: 168 WARNING @ Sun, 21 Jun 2020 21:16:55: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Sun, 21 Jun 2020 21:16:55: start model_add_line... INFO @ Sun, 21 Jun 2020 21:16:55: start X-correlation... INFO @ Sun, 21 Jun 2020 21:16:55: end of X-cor INFO @ Sun, 21 Jun 2020 21:16:55: #2 finished! INFO @ Sun, 21 Jun 2020 21:16:55: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 21:16:55: #2 alternative fragment length(s) may be 3,63,541,572 bps INFO @ Sun, 21 Jun 2020 21:16:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.10_model.r WARNING @ Sun, 21 Jun 2020 21:16:55: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:16:55: #2 You may need to consider one of the other alternative d(s): 3,63,541,572 WARNING @ Sun, 21 Jun 2020 21:16:55: #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 21:16:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:16:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:16:57: 15000000 INFO @ Sun, 21 Jun 2020 21:17:05: 16000000 INFO @ Sun, 21 Jun 2020 21:17:12: 17000000 INFO @ Sun, 21 Jun 2020 21:17:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:17:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:17:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.05_summits.bed INFO @ Sun, 21 Jun 2020 21:17:14: Done! pass1 - making usageList (290 chroms): 2 millis pass2 - checking and writing primary data (8144 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:17:18: 18000000 INFO @ Sun, 21 Jun 2020 21:17:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:17:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:17:23: #1 total tags in treatment: 18602259 INFO @ Sun, 21 Jun 2020 21:17:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:17:23: #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 21:17:24: #1 tags after filtering in treatment: 18602227 INFO @ Sun, 21 Jun 2020 21:17:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:17:24: #1 finished! INFO @ Sun, 21 Jun 2020 21:17:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:17:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:17:25: #2 number of paired peaks: 168 WARNING @ Sun, 21 Jun 2020 21:17:25: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Sun, 21 Jun 2020 21:17:25: start model_add_line... INFO @ Sun, 21 Jun 2020 21:17:25: start X-correlation... INFO @ Sun, 21 Jun 2020 21:17:25: end of X-cor INFO @ Sun, 21 Jun 2020 21:17:25: #2 finished! INFO @ Sun, 21 Jun 2020 21:17:25: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 21:17:25: #2 alternative fragment length(s) may be 3,63,541,572 bps INFO @ Sun, 21 Jun 2020 21:17:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.20_model.r WARNING @ Sun, 21 Jun 2020 21:17:25: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:17:25: #2 You may need to consider one of the other alternative d(s): 3,63,541,572 WARNING @ Sun, 21 Jun 2020 21:17:25: #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 21:17:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:17:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:17:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:17:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:17:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:17:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.10_summits.bed INFO @ Sun, 21 Jun 2020 21:17:49: Done! pass1 - making usageList (156 chroms): 1 millis pass2 - checking and writing primary data (2397 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:18:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:18:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:18:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:18:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669052/SRX4669052.20_summits.bed INFO @ Sun, 21 Jun 2020 21:18:18: Done! pass1 - making usageList (74 chroms): 1 millis pass2 - checking and writing primary data (217 records, 4 fields): 5 millis CompletedMACS2peakCalling