Job ID = 6498339 SRX = SRX485218 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:28:31 prefetch.2.10.7: 1) Downloading 'SRR1187976'... 2020-06-25T23:28:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:31:33 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:31:33 prefetch.2.10.7: 1) 'SRR1187976' was downloaded successfully 2020-06-25T23:31:33 prefetch.2.10.7: 'SRR1187976' has 0 unresolved dependencies Read 21943222 spots for SRR1187976/SRR1187976.sra Written 21943222 spots for SRR1187976/SRR1187976.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: 00:09:15 21943222 reads; of these: 21943222 (100.00%) were unpaired; of these: 857489 (3.91%) aligned 0 times 11136689 (50.75%) aligned exactly 1 time 9949044 (45.34%) aligned >1 times 96.09% overall alignment rate Time searching: 00:09:15 Overall time: 00:09:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3796691 / 21085733 = 0.1801 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 @ Fri, 26 Jun 2020 08:47:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.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 @ Fri, 26 Jun 2020 08:47:40: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:47:40: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:47:46: 1000000 INFO @ Fri, 26 Jun 2020 08:47:52: 2000000 INFO @ Fri, 26 Jun 2020 08:47:58: 3000000 INFO @ Fri, 26 Jun 2020 08:48:04: 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 @ Fri, 26 Jun 2020 08:48:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.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 @ Fri, 26 Jun 2020 08:48:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:48:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:48:10: 5000000 INFO @ Fri, 26 Jun 2020 08:48:15: 1000000 INFO @ Fri, 26 Jun 2020 08:48:16: 6000000 INFO @ Fri, 26 Jun 2020 08:48:21: 2000000 INFO @ Fri, 26 Jun 2020 08:48:23: 7000000 INFO @ Fri, 26 Jun 2020 08:48:26: 3000000 INFO @ Fri, 26 Jun 2020 08:48:29: 8000000 INFO @ Fri, 26 Jun 2020 08:48:32: 4000000 INFO @ Fri, 26 Jun 2020 08:48:35: 9000000 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 @ Fri, 26 Jun 2020 08:48:38: 5000000 INFO @ Fri, 26 Jun 2020 08:48:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.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 @ Fri, 26 Jun 2020 08:48:40: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:48:40: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:48:41: 10000000 INFO @ Fri, 26 Jun 2020 08:48:43: 6000000 INFO @ Fri, 26 Jun 2020 08:48:45: 1000000 INFO @ Fri, 26 Jun 2020 08:48:48: 11000000 INFO @ Fri, 26 Jun 2020 08:48:49: 7000000 INFO @ Fri, 26 Jun 2020 08:48:51: 2000000 INFO @ Fri, 26 Jun 2020 08:48:54: 12000000 INFO @ Fri, 26 Jun 2020 08:48:54: 8000000 INFO @ Fri, 26 Jun 2020 08:48:57: 3000000 INFO @ Fri, 26 Jun 2020 08:49:00: 9000000 INFO @ Fri, 26 Jun 2020 08:49:00: 13000000 INFO @ Fri, 26 Jun 2020 08:49:02: 4000000 INFO @ Fri, 26 Jun 2020 08:49:06: 10000000 INFO @ Fri, 26 Jun 2020 08:49:07: 14000000 INFO @ Fri, 26 Jun 2020 08:49:08: 5000000 INFO @ Fri, 26 Jun 2020 08:49:11: 11000000 INFO @ Fri, 26 Jun 2020 08:49:13: 15000000 INFO @ Fri, 26 Jun 2020 08:49:14: 6000000 INFO @ Fri, 26 Jun 2020 08:49:17: 12000000 INFO @ Fri, 26 Jun 2020 08:49:19: 16000000 INFO @ Fri, 26 Jun 2020 08:49:19: 7000000 INFO @ Fri, 26 Jun 2020 08:49:23: 13000000 INFO @ Fri, 26 Jun 2020 08:49:25: 8000000 INFO @ Fri, 26 Jun 2020 08:49:25: 17000000 INFO @ Fri, 26 Jun 2020 08:49:27: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:49:27: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:49:27: #1 total tags in treatment: 17289042 INFO @ Fri, 26 Jun 2020 08:49:27: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:49:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:49:27: #1 tags after filtering in treatment: 17289042 INFO @ Fri, 26 Jun 2020 08:49:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:49:27: #1 finished! INFO @ Fri, 26 Jun 2020 08:49:27: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:49:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:49:28: 14000000 INFO @ Fri, 26 Jun 2020 08:49:29: #2 number of paired peaks: 220 WARNING @ Fri, 26 Jun 2020 08:49:29: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Fri, 26 Jun 2020 08:49:29: start model_add_line... INFO @ Fri, 26 Jun 2020 08:49:29: start X-correlation... INFO @ Fri, 26 Jun 2020 08:49:29: end of X-cor INFO @ Fri, 26 Jun 2020 08:49:29: #2 finished! INFO @ Fri, 26 Jun 2020 08:49:29: #2 predicted fragment length is 66 bps INFO @ Fri, 26 Jun 2020 08:49:29: #2 alternative fragment length(s) may be 4,66 bps INFO @ Fri, 26 Jun 2020 08:49:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.05_model.r WARNING @ Fri, 26 Jun 2020 08:49:29: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:49:29: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Fri, 26 Jun 2020 08:49:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:49:29: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:49:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:49:30: 9000000 INFO @ Fri, 26 Jun 2020 08:49:34: 15000000 INFO @ Fri, 26 Jun 2020 08:49:36: 10000000 INFO @ Fri, 26 Jun 2020 08:49:39: 16000000 INFO @ Fri, 26 Jun 2020 08:49:41: 11000000 INFO @ Fri, 26 Jun 2020 08:49:45: 17000000 INFO @ Fri, 26 Jun 2020 08:49:47: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:49:47: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:49:47: #1 total tags in treatment: 17289042 INFO @ Fri, 26 Jun 2020 08:49:47: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:49:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:49:47: 12000000 INFO @ Fri, 26 Jun 2020 08:49:47: #1 tags after filtering in treatment: 17289042 INFO @ Fri, 26 Jun 2020 08:49:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:49:47: #1 finished! INFO @ Fri, 26 Jun 2020 08:49:47: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:49:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:49:48: #2 number of paired peaks: 220 WARNING @ Fri, 26 Jun 2020 08:49:48: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Fri, 26 Jun 2020 08:49:48: start model_add_line... INFO @ Fri, 26 Jun 2020 08:49:48: start X-correlation... INFO @ Fri, 26 Jun 2020 08:49:48: end of X-cor INFO @ Fri, 26 Jun 2020 08:49:48: #2 finished! INFO @ Fri, 26 Jun 2020 08:49:48: #2 predicted fragment length is 66 bps INFO @ Fri, 26 Jun 2020 08:49:48: #2 alternative fragment length(s) may be 4,66 bps INFO @ Fri, 26 Jun 2020 08:49:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.10_model.r WARNING @ Fri, 26 Jun 2020 08:49:48: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:49:48: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Fri, 26 Jun 2020 08:49:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:49:48: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:49:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:49:52: 13000000 INFO @ Fri, 26 Jun 2020 08:49:58: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:50:03: 15000000 INFO @ Fri, 26 Jun 2020 08:50:05: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:50:08: 16000000 INFO @ Fri, 26 Jun 2020 08:50:14: 17000000 INFO @ Fri, 26 Jun 2020 08:50:15: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:50:15: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:50:15: #1 total tags in treatment: 17289042 INFO @ Fri, 26 Jun 2020 08:50:15: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:50:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:50:16: #1 tags after filtering in treatment: 17289042 INFO @ Fri, 26 Jun 2020 08:50:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:50:16: #1 finished! INFO @ Fri, 26 Jun 2020 08:50:16: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:50:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:50:17: #2 number of paired peaks: 220 WARNING @ Fri, 26 Jun 2020 08:50:17: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Fri, 26 Jun 2020 08:50:17: start model_add_line... INFO @ Fri, 26 Jun 2020 08:50:17: start X-correlation... INFO @ Fri, 26 Jun 2020 08:50:17: end of X-cor INFO @ Fri, 26 Jun 2020 08:50:17: #2 finished! INFO @ Fri, 26 Jun 2020 08:50:17: #2 predicted fragment length is 66 bps INFO @ Fri, 26 Jun 2020 08:50:17: #2 alternative fragment length(s) may be 4,66 bps INFO @ Fri, 26 Jun 2020 08:50:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.20_model.r WARNING @ Fri, 26 Jun 2020 08:50:17: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:50:17: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Fri, 26 Jun 2020 08:50:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:50:17: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:50:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:50:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:50:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:50:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.05_summits.bed INFO @ Fri, 26 Jun 2020 08:50:23: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4999 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:50:24: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:50:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:50:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:50:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.10_summits.bed INFO @ Fri, 26 Jun 2020 08:50:42: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1691 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:50:52: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:51:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:51:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:51:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485218/SRX485218.20_summits.bed INFO @ Fri, 26 Jun 2020 08:51:10: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (515 records, 4 fields): 2 millis CompletedMACS2peakCalling