Job ID = 6452712 SRX = SRX026863 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:43:53 prefetch.2.10.7: 1) Downloading 'SRR065763'... 2020-06-21T07:43:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:46:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:46:19 prefetch.2.10.7: 'SRR065763' is valid 2020-06-21T07:46:19 prefetch.2.10.7: 1) 'SRR065763' was downloaded successfully Read 23105084 spots for SRR065763/SRR065763.sra Written 23105084 spots for SRR065763/SRR065763.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:36 23105084 reads; of these: 23105084 (100.00%) were unpaired; of these: 1043535 (4.52%) aligned 0 times 15481509 (67.00%) aligned exactly 1 time 6580040 (28.48%) aligned >1 times 95.48% overall alignment rate Time searching: 00:05:37 Overall time: 00:05:37 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] 4360787 / 22061549 = 0.1977 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 16:57:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.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 16:57:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:57:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:57:52: 1000000 INFO @ Sun, 21 Jun 2020 16:57:59: 2000000 INFO @ Sun, 21 Jun 2020 16:58:06: 3000000 INFO @ Sun, 21 Jun 2020 16:58:13: 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 16:58:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.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 16:58:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:58:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:58:20: 5000000 INFO @ Sun, 21 Jun 2020 16:58:22: 1000000 INFO @ Sun, 21 Jun 2020 16:58:27: 6000000 INFO @ Sun, 21 Jun 2020 16:58:29: 2000000 INFO @ Sun, 21 Jun 2020 16:58:35: 7000000 INFO @ Sun, 21 Jun 2020 16:58:36: 3000000 INFO @ Sun, 21 Jun 2020 16:58:42: 8000000 INFO @ Sun, 21 Jun 2020 16:58:43: 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 16:58:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.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 16:58:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:58:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:58:50: 9000000 INFO @ Sun, 21 Jun 2020 16:58:50: 5000000 INFO @ Sun, 21 Jun 2020 16:58:53: 1000000 INFO @ Sun, 21 Jun 2020 16:58:57: 6000000 INFO @ Sun, 21 Jun 2020 16:58:58: 10000000 INFO @ Sun, 21 Jun 2020 16:59:01: 2000000 INFO @ Sun, 21 Jun 2020 16:59:04: 7000000 INFO @ Sun, 21 Jun 2020 16:59:05: 11000000 INFO @ Sun, 21 Jun 2020 16:59:09: 3000000 INFO @ Sun, 21 Jun 2020 16:59:11: 8000000 INFO @ Sun, 21 Jun 2020 16:59:13: 12000000 INFO @ Sun, 21 Jun 2020 16:59:17: 4000000 INFO @ Sun, 21 Jun 2020 16:59:18: 9000000 INFO @ Sun, 21 Jun 2020 16:59:20: 13000000 INFO @ Sun, 21 Jun 2020 16:59:25: 5000000 INFO @ Sun, 21 Jun 2020 16:59:26: 10000000 INFO @ Sun, 21 Jun 2020 16:59:28: 14000000 INFO @ Sun, 21 Jun 2020 16:59:33: 11000000 INFO @ Sun, 21 Jun 2020 16:59:33: 6000000 INFO @ Sun, 21 Jun 2020 16:59:36: 15000000 INFO @ Sun, 21 Jun 2020 16:59:40: 12000000 INFO @ Sun, 21 Jun 2020 16:59:41: 7000000 INFO @ Sun, 21 Jun 2020 16:59:44: 16000000 INFO @ Sun, 21 Jun 2020 16:59:47: 13000000 INFO @ Sun, 21 Jun 2020 16:59:49: 8000000 INFO @ Sun, 21 Jun 2020 16:59:51: 17000000 INFO @ Sun, 21 Jun 2020 16:59:54: 14000000 INFO @ Sun, 21 Jun 2020 16:59:56: 9000000 INFO @ Sun, 21 Jun 2020 16:59:57: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:59:57: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:59:57: #1 total tags in treatment: 17700762 INFO @ Sun, 21 Jun 2020 16:59:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:59:57: #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 16:59:57: #1 tags after filtering in treatment: 17700758 INFO @ Sun, 21 Jun 2020 16:59:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:59:57: #1 finished! INFO @ Sun, 21 Jun 2020 16:59:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:59:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:59:59: #2 number of paired peaks: 860 WARNING @ Sun, 21 Jun 2020 16:59:59: Fewer paired peaks (860) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 860 pairs to build model! INFO @ Sun, 21 Jun 2020 16:59:59: start model_add_line... INFO @ Sun, 21 Jun 2020 16:59:59: start X-correlation... INFO @ Sun, 21 Jun 2020 16:59:59: end of X-cor INFO @ Sun, 21 Jun 2020 16:59:59: #2 finished! INFO @ Sun, 21 Jun 2020 16:59:59: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 16:59:59: #2 alternative fragment length(s) may be 3,45,84 bps INFO @ Sun, 21 Jun 2020 16:59:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.05_model.r WARNING @ Sun, 21 Jun 2020 16:59:59: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:59:59: #2 You may need to consider one of the other alternative d(s): 3,45,84 WARNING @ Sun, 21 Jun 2020 16:59:59: #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 16:59:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:59:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:00:01: 15000000 INFO @ Sun, 21 Jun 2020 17:00:04: 10000000 INFO @ Sun, 21 Jun 2020 17:00:08: 16000000 INFO @ Sun, 21 Jun 2020 17:00:11: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:00:15: 17000000 INFO @ Sun, 21 Jun 2020 17:00:18: 12000000 INFO @ Sun, 21 Jun 2020 17:00:20: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:00:20: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:00:20: #1 total tags in treatment: 17700762 INFO @ Sun, 21 Jun 2020 17:00:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:00:20: #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 17:00:21: #1 tags after filtering in treatment: 17700758 INFO @ Sun, 21 Jun 2020 17:00:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:00:21: #1 finished! INFO @ Sun, 21 Jun 2020 17:00:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:00:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:00:22: #2 number of paired peaks: 860 WARNING @ Sun, 21 Jun 2020 17:00:22: Fewer paired peaks (860) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 860 pairs to build model! INFO @ Sun, 21 Jun 2020 17:00:22: start model_add_line... INFO @ Sun, 21 Jun 2020 17:00:22: start X-correlation... INFO @ Sun, 21 Jun 2020 17:00:22: end of X-cor INFO @ Sun, 21 Jun 2020 17:00:22: #2 finished! INFO @ Sun, 21 Jun 2020 17:00:22: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 17:00:22: #2 alternative fragment length(s) may be 3,45,84 bps INFO @ Sun, 21 Jun 2020 17:00:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.10_model.r WARNING @ Sun, 21 Jun 2020 17:00:22: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:00:22: #2 You may need to consider one of the other alternative d(s): 3,45,84 WARNING @ Sun, 21 Jun 2020 17:00:22: #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 17:00:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:00:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:00:25: 13000000 INFO @ Sun, 21 Jun 2020 17:00:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:00:32: 14000000 INFO @ Sun, 21 Jun 2020 17:00:39: 15000000 INFO @ Sun, 21 Jun 2020 17:00:45: 16000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:00:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:00:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:00:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.05_summits.bed INFO @ Sun, 21 Jun 2020 17:00:49: Done! pass1 - making usageList (731 chroms): 2 millis pass2 - checking and writing primary data (4727 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:00:52: 17000000 INFO @ Sun, 21 Jun 2020 17:00:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:00:56: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:00:56: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:00:56: #1 total tags in treatment: 17700762 INFO @ Sun, 21 Jun 2020 17:00:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:00:56: #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 17:00:57: #1 tags after filtering in treatment: 17700758 INFO @ Sun, 21 Jun 2020 17:00:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:00:57: #1 finished! INFO @ Sun, 21 Jun 2020 17:00:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:00:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:00:58: #2 number of paired peaks: 860 WARNING @ Sun, 21 Jun 2020 17:00:58: Fewer paired peaks (860) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 860 pairs to build model! INFO @ Sun, 21 Jun 2020 17:00:58: start model_add_line... INFO @ Sun, 21 Jun 2020 17:00:58: start X-correlation... INFO @ Sun, 21 Jun 2020 17:00:58: end of X-cor INFO @ Sun, 21 Jun 2020 17:00:58: #2 finished! INFO @ Sun, 21 Jun 2020 17:00:58: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 17:00:58: #2 alternative fragment length(s) may be 3,45,84 bps INFO @ Sun, 21 Jun 2020 17:00:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.20_model.r WARNING @ Sun, 21 Jun 2020 17:00:58: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:00:58: #2 You may need to consider one of the other alternative d(s): 3,45,84 WARNING @ Sun, 21 Jun 2020 17:00:58: #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 17:00:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:00:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:01:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:01:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:01:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.10_summits.bed INFO @ Sun, 21 Jun 2020 17:01:13: Done! pass1 - making usageList (634 chroms): 2 millis pass2 - checking and writing primary data (2863 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:01:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:01:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:01:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:01:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX026863/SRX026863.20_summits.bed INFO @ Sun, 21 Jun 2020 17:01:46: Done! pass1 - making usageList (453 chroms): 1 millis pass2 - checking and writing primary data (1368 records, 4 fields): 17 millis CompletedMACS2peakCalling