Job ID = 6455234 SRX = SRX287579 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:47:40 prefetch.2.10.7: 1) Downloading 'SRR869722'... 2020-06-21T09:47:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:51:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:51:00 prefetch.2.10.7: 1) 'SRR869722' was downloaded successfully Read 19172821 spots for SRR869722/SRR869722.sra Written 19172821 spots for SRR869722/SRR869722.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: 00:05:47 19172821 reads; of these: 19172821 (100.00%) were unpaired; of these: 908416 (4.74%) aligned 0 times 12595425 (65.69%) aligned exactly 1 time 5668980 (29.57%) aligned >1 times 95.26% overall alignment rate Time searching: 00:05:47 Overall time: 00:05:47 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] 3545209 / 18264405 = 0.1941 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 19:02:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.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 19:02:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:02:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:02:32: 1000000 INFO @ Sun, 21 Jun 2020 19:02:38: 2000000 INFO @ Sun, 21 Jun 2020 19:02:43: 3000000 INFO @ Sun, 21 Jun 2020 19:02:49: 4000000 INFO @ Sun, 21 Jun 2020 19:02:54: 5000000 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 19:02:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.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 19:02:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:02:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:03:00: 6000000 INFO @ Sun, 21 Jun 2020 19:03:04: 1000000 INFO @ Sun, 21 Jun 2020 19:03:07: 7000000 INFO @ Sun, 21 Jun 2020 19:03:12: 2000000 INFO @ Sun, 21 Jun 2020 19:03:14: 8000000 INFO @ Sun, 21 Jun 2020 19:03:20: 3000000 INFO @ Sun, 21 Jun 2020 19:03:20: 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 @ Sun, 21 Jun 2020 19:03:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.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 19:03:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:03:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:03:27: 10000000 INFO @ Sun, 21 Jun 2020 19:03:27: 4000000 INFO @ Sun, 21 Jun 2020 19:03:33: 1000000 INFO @ Sun, 21 Jun 2020 19:03:33: 11000000 INFO @ Sun, 21 Jun 2020 19:03:35: 5000000 INFO @ Sun, 21 Jun 2020 19:03:40: 2000000 INFO @ Sun, 21 Jun 2020 19:03:41: 12000000 INFO @ Sun, 21 Jun 2020 19:03:42: 6000000 INFO @ Sun, 21 Jun 2020 19:03:47: 3000000 INFO @ Sun, 21 Jun 2020 19:03:47: 13000000 INFO @ Sun, 21 Jun 2020 19:03:50: 7000000 INFO @ Sun, 21 Jun 2020 19:03:54: 4000000 INFO @ Sun, 21 Jun 2020 19:03:54: 14000000 INFO @ Sun, 21 Jun 2020 19:03:57: 8000000 INFO @ Sun, 21 Jun 2020 19:03:59: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:03:59: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:03:59: #1 total tags in treatment: 14719196 INFO @ Sun, 21 Jun 2020 19:03:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:03:59: #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 19:04:00: #1 tags after filtering in treatment: 14719196 INFO @ Sun, 21 Jun 2020 19:04:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:00: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:04:00: 5000000 INFO @ Sun, 21 Jun 2020 19:04:01: #2 number of paired peaks: 700 WARNING @ Sun, 21 Jun 2020 19:04:01: Fewer paired peaks (700) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 700 pairs to build model! INFO @ Sun, 21 Jun 2020 19:04:01: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:01: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:01: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:01: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:01: #2 predicted fragment length is 36 bps INFO @ Sun, 21 Jun 2020 19:04:01: #2 alternative fragment length(s) may be 3,36 bps INFO @ Sun, 21 Jun 2020 19:04:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.05_model.r WARNING @ Sun, 21 Jun 2020 19:04:01: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:04:01: #2 You may need to consider one of the other alternative d(s): 3,36 WARNING @ Sun, 21 Jun 2020 19:04:01: #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 19:04:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:04:05: 9000000 INFO @ Sun, 21 Jun 2020 19:04:07: 6000000 INFO @ Sun, 21 Jun 2020 19:04:13: 10000000 INFO @ Sun, 21 Jun 2020 19:04:14: 7000000 INFO @ Sun, 21 Jun 2020 19:04:20: 11000000 INFO @ Sun, 21 Jun 2020 19:04:21: 8000000 INFO @ Sun, 21 Jun 2020 19:04:27: 9000000 INFO @ Sun, 21 Jun 2020 19:04:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:04:28: 12000000 INFO @ Sun, 21 Jun 2020 19:04:34: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:04:36: 13000000 INFO @ Sun, 21 Jun 2020 19:04:41: 11000000 INFO @ Sun, 21 Jun 2020 19:04:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:04:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:04:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.05_summits.bed INFO @ Sun, 21 Jun 2020 19:04:42: Done! pass1 - making usageList (649 chroms): 2 millis pass2 - checking and writing primary data (2398 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:04:43: 14000000 INFO @ Sun, 21 Jun 2020 19:04:48: 12000000 INFO @ Sun, 21 Jun 2020 19:04:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:04:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:04:49: #1 total tags in treatment: 14719196 INFO @ Sun, 21 Jun 2020 19:04:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:49: #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 19:04:49: #1 tags after filtering in treatment: 14719196 INFO @ Sun, 21 Jun 2020 19:04:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:49: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:04:50: #2 number of paired peaks: 700 WARNING @ Sun, 21 Jun 2020 19:04:50: Fewer paired peaks (700) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 700 pairs to build model! INFO @ Sun, 21 Jun 2020 19:04:50: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:50: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:50: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:50: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:50: #2 predicted fragment length is 36 bps INFO @ Sun, 21 Jun 2020 19:04:50: #2 alternative fragment length(s) may be 3,36 bps INFO @ Sun, 21 Jun 2020 19:04:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.10_model.r WARNING @ Sun, 21 Jun 2020 19:04:50: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:04:50: #2 You may need to consider one of the other alternative d(s): 3,36 WARNING @ Sun, 21 Jun 2020 19:04:50: #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 19:04:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:04:54: 13000000 INFO @ Sun, 21 Jun 2020 19:04:59: 14000000 INFO @ Sun, 21 Jun 2020 19:05:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:05:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:05:04: #1 total tags in treatment: 14719196 INFO @ Sun, 21 Jun 2020 19:05:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:05:04: #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 19:05:04: #1 tags after filtering in treatment: 14719196 INFO @ Sun, 21 Jun 2020 19:05:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:05:04: #1 finished! INFO @ Sun, 21 Jun 2020 19:05:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:05:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:05:05: #2 number of paired peaks: 700 WARNING @ Sun, 21 Jun 2020 19:05:05: Fewer paired peaks (700) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 700 pairs to build model! INFO @ Sun, 21 Jun 2020 19:05:05: start model_add_line... INFO @ Sun, 21 Jun 2020 19:05:05: start X-correlation... INFO @ Sun, 21 Jun 2020 19:05:05: end of X-cor INFO @ Sun, 21 Jun 2020 19:05:05: #2 finished! INFO @ Sun, 21 Jun 2020 19:05:05: #2 predicted fragment length is 36 bps INFO @ Sun, 21 Jun 2020 19:05:05: #2 alternative fragment length(s) may be 3,36 bps INFO @ Sun, 21 Jun 2020 19:05:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.20_model.r WARNING @ Sun, 21 Jun 2020 19:05:05: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:05:05: #2 You may need to consider one of the other alternative d(s): 3,36 WARNING @ Sun, 21 Jun 2020 19:05:05: #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 19:05:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:05:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:05:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:05:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.10_summits.bed INFO @ Sun, 21 Jun 2020 19:05:32: Done! INFO @ Sun, 21 Jun 2020 19:05:33: #3 Call peaks for each chromosome... pass1 - making usageList (502 chroms): 1 millis pass2 - checking and writing primary data (1982 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:05:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287579/SRX287579.20_summits.bed INFO @ Sun, 21 Jun 2020 19:05:47: Done! pass1 - making usageList (356 chroms): 1 millis pass2 - checking and writing primary data (830 records, 4 fields): 11 millis CompletedMACS2peakCalling