Job ID = 6452681 SRX = SRX025483 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:59:53 prefetch.2.10.7: 1) Downloading 'SRR063886'... 2020-06-21T07:59:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:02:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:02:01 prefetch.2.10.7: 'SRR063886' is valid 2020-06-21T08:02:01 prefetch.2.10.7: 1) 'SRR063886' was downloaded successfully Read 27979833 spots for SRR063886/SRR063886.sra Written 27979833 spots for SRR063886/SRR063886.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: 00:06:11 27979833 reads; of these: 27979833 (100.00%) were unpaired; of these: 819161 (2.93%) aligned 0 times 20440269 (73.05%) aligned exactly 1 time 6720403 (24.02%) aligned >1 times 97.07% overall alignment rate Time searching: 00:06:11 Overall time: 00:06:11 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] 4930664 / 27160672 = 0.1815 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 17:14:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.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 17:14:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:14:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:14:05: 1000000 INFO @ Sun, 21 Jun 2020 17:14:09: 2000000 INFO @ Sun, 21 Jun 2020 17:14:14: 3000000 INFO @ Sun, 21 Jun 2020 17:14:18: 4000000 INFO @ Sun, 21 Jun 2020 17:14:23: 5000000 INFO @ Sun, 21 Jun 2020 17:14:27: 6000000 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 17:14:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.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 17:14:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:14:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:14:32: 7000000 INFO @ Sun, 21 Jun 2020 17:14:35: 1000000 INFO @ Sun, 21 Jun 2020 17:14:36: 8000000 INFO @ Sun, 21 Jun 2020 17:14:40: 2000000 INFO @ Sun, 21 Jun 2020 17:14:41: 9000000 INFO @ Sun, 21 Jun 2020 17:14:45: 3000000 INFO @ Sun, 21 Jun 2020 17:14:46: 10000000 INFO @ Sun, 21 Jun 2020 17:14:49: 4000000 INFO @ Sun, 21 Jun 2020 17:14:50: 11000000 INFO @ Sun, 21 Jun 2020 17:14:54: 5000000 INFO @ Sun, 21 Jun 2020 17:14:55: 12000000 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 17:14:59: 6000000 INFO @ Sun, 21 Jun 2020 17:14:59: 13000000 INFO @ Sun, 21 Jun 2020 17:15:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.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 17:15:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:15:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:15:04: 7000000 INFO @ Sun, 21 Jun 2020 17:15:04: 14000000 INFO @ Sun, 21 Jun 2020 17:15:05: 1000000 INFO @ Sun, 21 Jun 2020 17:15:08: 8000000 INFO @ Sun, 21 Jun 2020 17:15:09: 15000000 INFO @ Sun, 21 Jun 2020 17:15:10: 2000000 INFO @ Sun, 21 Jun 2020 17:15:13: 9000000 INFO @ Sun, 21 Jun 2020 17:15:13: 16000000 INFO @ Sun, 21 Jun 2020 17:15:15: 3000000 INFO @ Sun, 21 Jun 2020 17:15:18: 10000000 INFO @ Sun, 21 Jun 2020 17:15:18: 17000000 INFO @ Sun, 21 Jun 2020 17:15:19: 4000000 INFO @ Sun, 21 Jun 2020 17:15:23: 11000000 INFO @ Sun, 21 Jun 2020 17:15:23: 18000000 INFO @ Sun, 21 Jun 2020 17:15:24: 5000000 INFO @ Sun, 21 Jun 2020 17:15:27: 12000000 INFO @ Sun, 21 Jun 2020 17:15:28: 19000000 INFO @ Sun, 21 Jun 2020 17:15:29: 6000000 INFO @ Sun, 21 Jun 2020 17:15:32: 13000000 INFO @ Sun, 21 Jun 2020 17:15:32: 20000000 INFO @ Sun, 21 Jun 2020 17:15:34: 7000000 INFO @ Sun, 21 Jun 2020 17:15:37: 14000000 INFO @ Sun, 21 Jun 2020 17:15:37: 21000000 INFO @ Sun, 21 Jun 2020 17:15:38: 8000000 INFO @ Sun, 21 Jun 2020 17:15:42: 15000000 INFO @ Sun, 21 Jun 2020 17:15:42: 22000000 INFO @ Sun, 21 Jun 2020 17:15:43: 9000000 INFO @ Sun, 21 Jun 2020 17:15:43: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:15:43: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:15:43: #1 total tags in treatment: 22230008 INFO @ Sun, 21 Jun 2020 17:15:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:15:43: #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 17:15:44: #1 tags after filtering in treatment: 22230008 INFO @ Sun, 21 Jun 2020 17:15:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:15:44: #1 finished! INFO @ Sun, 21 Jun 2020 17:15:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:15:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:15:45: #2 number of paired peaks: 185 WARNING @ Sun, 21 Jun 2020 17:15:45: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sun, 21 Jun 2020 17:15:45: start model_add_line... INFO @ Sun, 21 Jun 2020 17:15:45: start X-correlation... INFO @ Sun, 21 Jun 2020 17:15:45: end of X-cor INFO @ Sun, 21 Jun 2020 17:15:45: #2 finished! INFO @ Sun, 21 Jun 2020 17:15:45: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 17:15:45: #2 alternative fragment length(s) may be 4,48,65,94 bps INFO @ Sun, 21 Jun 2020 17:15:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.05_model.r WARNING @ Sun, 21 Jun 2020 17:15:45: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:15:45: #2 You may need to consider one of the other alternative d(s): 4,48,65,94 WARNING @ Sun, 21 Jun 2020 17:15:45: #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 17:15:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:15:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:15:46: 16000000 INFO @ Sun, 21 Jun 2020 17:15:48: 10000000 INFO @ Sun, 21 Jun 2020 17:15:51: 17000000 INFO @ Sun, 21 Jun 2020 17:15:52: 11000000 INFO @ Sun, 21 Jun 2020 17:15:56: 18000000 INFO @ Sun, 21 Jun 2020 17:15:57: 12000000 INFO @ Sun, 21 Jun 2020 17:16:01: 19000000 INFO @ Sun, 21 Jun 2020 17:16:02: 13000000 INFO @ Sun, 21 Jun 2020 17:16:05: 20000000 INFO @ Sun, 21 Jun 2020 17:16:06: 14000000 INFO @ Sun, 21 Jun 2020 17:16:10: 21000000 INFO @ Sun, 21 Jun 2020 17:16:11: 15000000 INFO @ Sun, 21 Jun 2020 17:16:15: 22000000 INFO @ Sun, 21 Jun 2020 17:16:16: 16000000 INFO @ Sun, 21 Jun 2020 17:16:16: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:16:16: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:16:16: #1 total tags in treatment: 22230008 INFO @ Sun, 21 Jun 2020 17:16:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:16:16: #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 17:16:17: #1 tags after filtering in treatment: 22230008 INFO @ Sun, 21 Jun 2020 17:16:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:16:17: #1 finished! INFO @ Sun, 21 Jun 2020 17:16:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:16:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:16:18: #2 number of paired peaks: 185 WARNING @ Sun, 21 Jun 2020 17:16:18: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sun, 21 Jun 2020 17:16:18: start model_add_line... INFO @ Sun, 21 Jun 2020 17:16:18: start X-correlation... INFO @ Sun, 21 Jun 2020 17:16:18: end of X-cor INFO @ Sun, 21 Jun 2020 17:16:18: #2 finished! INFO @ Sun, 21 Jun 2020 17:16:18: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 17:16:18: #2 alternative fragment length(s) may be 4,48,65,94 bps INFO @ Sun, 21 Jun 2020 17:16:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.10_model.r WARNING @ Sun, 21 Jun 2020 17:16:18: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:16:18: #2 You may need to consider one of the other alternative d(s): 4,48,65,94 WARNING @ Sun, 21 Jun 2020 17:16:18: #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 17:16:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:16:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:16:20: 17000000 INFO @ Sun, 21 Jun 2020 17:16:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:16:25: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:16:30: 19000000 INFO @ Sun, 21 Jun 2020 17:16:34: 20000000 INFO @ Sun, 21 Jun 2020 17:16:39: 21000000 INFO @ Sun, 21 Jun 2020 17:16:43: 22000000 INFO @ Sun, 21 Jun 2020 17:16:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:16:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:16:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.05_summits.bed INFO @ Sun, 21 Jun 2020 17:16:44: Done! pass1 - making usageList (528 chroms): 1 millis pass2 - checking and writing primary data (2165 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:16:44: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:16:44: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:16:44: #1 total tags in treatment: 22230008 INFO @ Sun, 21 Jun 2020 17:16:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:16:44: #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 17:16:45: #1 tags after filtering in treatment: 22230008 INFO @ Sun, 21 Jun 2020 17:16:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:16:45: #1 finished! INFO @ Sun, 21 Jun 2020 17:16:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:16:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:16:46: #2 number of paired peaks: 185 WARNING @ Sun, 21 Jun 2020 17:16:46: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sun, 21 Jun 2020 17:16:46: start model_add_line... INFO @ Sun, 21 Jun 2020 17:16:47: start X-correlation... INFO @ Sun, 21 Jun 2020 17:16:47: end of X-cor INFO @ Sun, 21 Jun 2020 17:16:47: #2 finished! INFO @ Sun, 21 Jun 2020 17:16:47: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 17:16:47: #2 alternative fragment length(s) may be 4,48,65,94 bps INFO @ Sun, 21 Jun 2020 17:16:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.20_model.r WARNING @ Sun, 21 Jun 2020 17:16:47: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:16:47: #2 You may need to consider one of the other alternative d(s): 4,48,65,94 WARNING @ Sun, 21 Jun 2020 17:16:47: #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 17:16:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:16:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:16:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:17:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:17:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:17:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.10_summits.bed INFO @ Sun, 21 Jun 2020 17:17:15: Done! pass1 - making usageList (417 chroms): 1 millis pass2 - checking and writing primary data (1660 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:17:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:17:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:17:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:17:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025483/SRX025483.20_summits.bed INFO @ Sun, 21 Jun 2020 17:17:45: Done! pass1 - making usageList (171 chroms): 1 millis pass2 - checking and writing primary data (362 records, 4 fields): 23 millis CompletedMACS2peakCalling