Job ID = 6527954 SRX = SRX3380810 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:07:50 prefetch.2.10.7: 1) Downloading 'SRR6278173'... 2020-06-29T14:07:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:11:37 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:11:37 prefetch.2.10.7: 1) 'SRR6278173' was downloaded successfully Read 27322220 spots for SRR6278173/SRR6278173.sra Written 27322220 spots for SRR6278173/SRR6278173.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: 00:11:04 27322220 reads; of these: 27322220 (100.00%) were unpaired; of these: 984425 (3.60%) aligned 0 times 18441906 (67.50%) aligned exactly 1 time 7895889 (28.90%) aligned >1 times 96.40% overall alignment rate Time searching: 00:11:04 Overall time: 00:11:04 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] 3731758 / 26337795 = 0.1417 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 @ Mon, 29 Jun 2020 23:39:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.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 @ Mon, 29 Jun 2020 23:39:24: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:39:24: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:39:30: 1000000 INFO @ Mon, 29 Jun 2020 23:39:35: 2000000 INFO @ Mon, 29 Jun 2020 23:39:41: 3000000 INFO @ Mon, 29 Jun 2020 23:39:46: 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 @ Mon, 29 Jun 2020 23:39:52: 5000000 INFO @ Mon, 29 Jun 2020 23:39:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.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 @ Mon, 29 Jun 2020 23:39:54: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:39:54: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:39:58: 6000000 INFO @ Mon, 29 Jun 2020 23:40:00: 1000000 INFO @ Mon, 29 Jun 2020 23:40:04: 7000000 INFO @ Mon, 29 Jun 2020 23:40:06: 2000000 INFO @ Mon, 29 Jun 2020 23:40:10: 8000000 INFO @ Mon, 29 Jun 2020 23:40:12: 3000000 INFO @ Mon, 29 Jun 2020 23:40:16: 9000000 INFO @ Mon, 29 Jun 2020 23:40:18: 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 @ Mon, 29 Jun 2020 23:40:22: 10000000 INFO @ Mon, 29 Jun 2020 23:40:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.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 @ Mon, 29 Jun 2020 23:40:24: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:40:24: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:40:24: 5000000 INFO @ Mon, 29 Jun 2020 23:40:28: 11000000 INFO @ Mon, 29 Jun 2020 23:40:30: 1000000 INFO @ Mon, 29 Jun 2020 23:40:30: 6000000 INFO @ Mon, 29 Jun 2020 23:40:34: 12000000 INFO @ Mon, 29 Jun 2020 23:40:36: 2000000 INFO @ Mon, 29 Jun 2020 23:40:36: 7000000 INFO @ Mon, 29 Jun 2020 23:40:40: 13000000 INFO @ Mon, 29 Jun 2020 23:40:42: 3000000 INFO @ Mon, 29 Jun 2020 23:40:42: 8000000 INFO @ Mon, 29 Jun 2020 23:40:46: 14000000 INFO @ Mon, 29 Jun 2020 23:40:47: 4000000 INFO @ Mon, 29 Jun 2020 23:40:49: 9000000 INFO @ Mon, 29 Jun 2020 23:40:52: 15000000 INFO @ Mon, 29 Jun 2020 23:40:53: 5000000 INFO @ Mon, 29 Jun 2020 23:40:55: 10000000 INFO @ Mon, 29 Jun 2020 23:40:58: 16000000 INFO @ Mon, 29 Jun 2020 23:40:59: 6000000 INFO @ Mon, 29 Jun 2020 23:41:01: 11000000 INFO @ Mon, 29 Jun 2020 23:41:04: 17000000 INFO @ Mon, 29 Jun 2020 23:41:05: 7000000 INFO @ Mon, 29 Jun 2020 23:41:07: 12000000 INFO @ Mon, 29 Jun 2020 23:41:10: 18000000 INFO @ Mon, 29 Jun 2020 23:41:11: 8000000 INFO @ Mon, 29 Jun 2020 23:41:13: 13000000 INFO @ Mon, 29 Jun 2020 23:41:16: 19000000 INFO @ Mon, 29 Jun 2020 23:41:16: 9000000 INFO @ Mon, 29 Jun 2020 23:41:19: 14000000 INFO @ Mon, 29 Jun 2020 23:41:22: 20000000 INFO @ Mon, 29 Jun 2020 23:41:22: 10000000 INFO @ Mon, 29 Jun 2020 23:41:25: 15000000 INFO @ Mon, 29 Jun 2020 23:41:28: 21000000 INFO @ Mon, 29 Jun 2020 23:41:28: 11000000 INFO @ Mon, 29 Jun 2020 23:41:31: 16000000 INFO @ Mon, 29 Jun 2020 23:41:34: 12000000 INFO @ Mon, 29 Jun 2020 23:41:34: 22000000 INFO @ Mon, 29 Jun 2020 23:41:37: 17000000 INFO @ Mon, 29 Jun 2020 23:41:38: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 23:41:38: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 23:41:38: #1 total tags in treatment: 22606037 INFO @ Mon, 29 Jun 2020 23:41:38: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:41:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:41:38: #1 tags after filtering in treatment: 22606037 INFO @ Mon, 29 Jun 2020 23:41:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:41:38: #1 finished! INFO @ Mon, 29 Jun 2020 23:41:38: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:41:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:41:39: 13000000 INFO @ Mon, 29 Jun 2020 23:41:40: #2 number of paired peaks: 139 WARNING @ Mon, 29 Jun 2020 23:41:40: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Mon, 29 Jun 2020 23:41:40: start model_add_line... INFO @ Mon, 29 Jun 2020 23:41:40: start X-correlation... INFO @ Mon, 29 Jun 2020 23:41:40: end of X-cor INFO @ Mon, 29 Jun 2020 23:41:40: #2 finished! INFO @ Mon, 29 Jun 2020 23:41:40: #2 predicted fragment length is 42 bps INFO @ Mon, 29 Jun 2020 23:41:40: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 29 Jun 2020 23:41:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.05_model.r WARNING @ Mon, 29 Jun 2020 23:41:40: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:41:40: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 29 Jun 2020 23:41:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:41:40: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:41:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:41:42: 18000000 INFO @ Mon, 29 Jun 2020 23:41:45: 14000000 INFO @ Mon, 29 Jun 2020 23:41:48: 19000000 INFO @ Mon, 29 Jun 2020 23:41:51: 15000000 INFO @ Mon, 29 Jun 2020 23:41:53: 20000000 INFO @ Mon, 29 Jun 2020 23:41:57: 16000000 INFO @ Mon, 29 Jun 2020 23:41:59: 21000000 INFO @ Mon, 29 Jun 2020 23:42:03: 17000000 INFO @ Mon, 29 Jun 2020 23:42:04: 22000000 INFO @ Mon, 29 Jun 2020 23:42:07: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 23:42:07: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 23:42:07: #1 total tags in treatment: 22606037 INFO @ Mon, 29 Jun 2020 23:42:07: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:42:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:42:08: #1 tags after filtering in treatment: 22606037 INFO @ Mon, 29 Jun 2020 23:42:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:42:08: #1 finished! INFO @ Mon, 29 Jun 2020 23:42:08: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:42:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:42:09: 18000000 INFO @ Mon, 29 Jun 2020 23:42:09: #2 number of paired peaks: 139 WARNING @ Mon, 29 Jun 2020 23:42:09: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Mon, 29 Jun 2020 23:42:09: start model_add_line... INFO @ Mon, 29 Jun 2020 23:42:09: start X-correlation... INFO @ Mon, 29 Jun 2020 23:42:09: end of X-cor INFO @ Mon, 29 Jun 2020 23:42:09: #2 finished! INFO @ Mon, 29 Jun 2020 23:42:09: #2 predicted fragment length is 42 bps INFO @ Mon, 29 Jun 2020 23:42:09: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 29 Jun 2020 23:42:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.10_model.r WARNING @ Mon, 29 Jun 2020 23:42:10: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:42:10: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 29 Jun 2020 23:42:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:42:10: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:42:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:42:15: 19000000 INFO @ Mon, 29 Jun 2020 23:42:16: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:42:21: 20000000 INFO @ Mon, 29 Jun 2020 23:42:27: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:42:33: 22000000 INFO @ Mon, 29 Jun 2020 23:42:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:42:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:42:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.05_summits.bed INFO @ Mon, 29 Jun 2020 23:42:36: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1887 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:42:36: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 23:42:36: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 23:42:36: #1 total tags in treatment: 22606037 INFO @ Mon, 29 Jun 2020 23:42:36: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:42:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:42:37: #1 tags after filtering in treatment: 22606037 INFO @ Mon, 29 Jun 2020 23:42:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:42:37: #1 finished! INFO @ Mon, 29 Jun 2020 23:42:37: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:42:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:42:38: #2 number of paired peaks: 139 WARNING @ Mon, 29 Jun 2020 23:42:38: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Mon, 29 Jun 2020 23:42:38: start model_add_line... INFO @ Mon, 29 Jun 2020 23:42:38: start X-correlation... INFO @ Mon, 29 Jun 2020 23:42:38: end of X-cor INFO @ Mon, 29 Jun 2020 23:42:38: #2 finished! INFO @ Mon, 29 Jun 2020 23:42:38: #2 predicted fragment length is 42 bps INFO @ Mon, 29 Jun 2020 23:42:38: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 29 Jun 2020 23:42:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.20_model.r WARNING @ Mon, 29 Jun 2020 23:42:38: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:42:38: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 29 Jun 2020 23:42:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:42:38: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:42:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:42:46: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:43:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:43:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:43:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.10_summits.bed INFO @ Mon, 29 Jun 2020 23:43:05: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1552 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:43:15: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:43:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:43:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:43:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3380810/SRX3380810.20_summits.bed INFO @ Mon, 29 Jun 2020 23:43:34: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1139 records, 4 fields): 3 millis CompletedMACS2peakCalling