Job ID = 6453361 SRX = SRX1120693 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:18:47 prefetch.2.10.7: 1) Downloading 'SRR2129925'... 2020-06-21T08:18:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:27:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:27:59 prefetch.2.10.7: 1) 'SRR2129925' was downloaded successfully Read 18274071 spots for SRR2129925/SRR2129925.sra Written 18274071 spots for SRR2129925/SRR2129925.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: 00:08:56 18274071 reads; of these: 18274071 (100.00%) were unpaired; of these: 1548147 (8.47%) aligned 0 times 5555709 (30.40%) aligned exactly 1 time 11170215 (61.13%) aligned >1 times 91.53% overall alignment rate Time searching: 00:08:56 Overall time: 00:08:56 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] 7552426 / 16725924 = 0.4515 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 17:42:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.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 17:42:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:42:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:43:01: 1000000 INFO @ Sun, 21 Jun 2020 17:43:07: 2000000 INFO @ Sun, 21 Jun 2020 17:43:14: 3000000 INFO @ Sun, 21 Jun 2020 17:43:20: 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 17:43:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.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 17:43:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:43:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:43:27: 5000000 INFO @ Sun, 21 Jun 2020 17:43:32: 1000000 INFO @ Sun, 21 Jun 2020 17:43:34: 6000000 INFO @ Sun, 21 Jun 2020 17:43:39: 2000000 INFO @ Sun, 21 Jun 2020 17:43:42: 7000000 INFO @ Sun, 21 Jun 2020 17:43:46: 3000000 INFO @ Sun, 21 Jun 2020 17:43:49: 8000000 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 17:43:54: 4000000 INFO @ Sun, 21 Jun 2020 17:43:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.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 17:43:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:43:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:43:57: 9000000 INFO @ Sun, 21 Jun 2020 17:43:58: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:43:58: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:43:58: #1 total tags in treatment: 9173498 INFO @ Sun, 21 Jun 2020 17:43:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:43:58: #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 17:43:58: #1 tags after filtering in treatment: 9173443 INFO @ Sun, 21 Jun 2020 17:43:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:43:58: #1 finished! INFO @ Sun, 21 Jun 2020 17:43:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:43:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:43:59: #2 number of paired peaks: 4893 INFO @ Sun, 21 Jun 2020 17:43:59: start model_add_line... INFO @ Sun, 21 Jun 2020 17:44:00: start X-correlation... INFO @ Sun, 21 Jun 2020 17:44:00: end of X-cor INFO @ Sun, 21 Jun 2020 17:44:00: #2 finished! INFO @ Sun, 21 Jun 2020 17:44:00: #2 predicted fragment length is 81 bps INFO @ Sun, 21 Jun 2020 17:44:00: #2 alternative fragment length(s) may be 3,81 bps INFO @ Sun, 21 Jun 2020 17:44:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.05_model.r WARNING @ Sun, 21 Jun 2020 17:44:00: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:44:00: #2 You may need to consider one of the other alternative d(s): 3,81 WARNING @ Sun, 21 Jun 2020 17:44:00: #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 17:44:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:44:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:44:02: 5000000 INFO @ Sun, 21 Jun 2020 17:44:03: 1000000 INFO @ Sun, 21 Jun 2020 17:44:09: 6000000 INFO @ Sun, 21 Jun 2020 17:44:10: 2000000 INFO @ Sun, 21 Jun 2020 17:44:17: 7000000 INFO @ Sun, 21 Jun 2020 17:44:18: 3000000 INFO @ Sun, 21 Jun 2020 17:44:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:44:25: 8000000 INFO @ Sun, 21 Jun 2020 17:44:25: 4000000 INFO @ Sun, 21 Jun 2020 17:44:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:44:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:44:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.05_summits.bed INFO @ Sun, 21 Jun 2020 17:44:28: Done! pass1 - making usageList (1057 chroms): 2 millis pass2 - checking and writing primary data (4330 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:44:33: 9000000 INFO @ Sun, 21 Jun 2020 17:44:33: 5000000 INFO @ Sun, 21 Jun 2020 17:44:34: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:44:34: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:44:34: #1 total tags in treatment: 9173498 INFO @ Sun, 21 Jun 2020 17:44:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:44:34: #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 17:44:35: #1 tags after filtering in treatment: 9173443 INFO @ Sun, 21 Jun 2020 17:44:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:44:35: #1 finished! INFO @ Sun, 21 Jun 2020 17:44:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:44:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:44:36: #2 number of paired peaks: 4893 INFO @ Sun, 21 Jun 2020 17:44:36: start model_add_line... INFO @ Sun, 21 Jun 2020 17:44:36: start X-correlation... INFO @ Sun, 21 Jun 2020 17:44:36: end of X-cor INFO @ Sun, 21 Jun 2020 17:44:36: #2 finished! INFO @ Sun, 21 Jun 2020 17:44:36: #2 predicted fragment length is 81 bps INFO @ Sun, 21 Jun 2020 17:44:36: #2 alternative fragment length(s) may be 3,81 bps INFO @ Sun, 21 Jun 2020 17:44:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.10_model.r WARNING @ Sun, 21 Jun 2020 17:44:36: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:44:36: #2 You may need to consider one of the other alternative d(s): 3,81 WARNING @ Sun, 21 Jun 2020 17:44:36: #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 17:44:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:44:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:44:40: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:44:48: 7000000 INFO @ Sun, 21 Jun 2020 17:44:54: 8000000 INFO @ Sun, 21 Jun 2020 17:44:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:45:01: 9000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:45:02: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:45:02: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:45:02: #1 total tags in treatment: 9173498 INFO @ Sun, 21 Jun 2020 17:45:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:45:02: #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 17:45:02: #1 tags after filtering in treatment: 9173443 INFO @ Sun, 21 Jun 2020 17:45:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:45:02: #1 finished! INFO @ Sun, 21 Jun 2020 17:45:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:45:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:45:03: #2 number of paired peaks: 4893 INFO @ Sun, 21 Jun 2020 17:45:03: start model_add_line... INFO @ Sun, 21 Jun 2020 17:45:03: start X-correlation... INFO @ Sun, 21 Jun 2020 17:45:03: end of X-cor INFO @ Sun, 21 Jun 2020 17:45:03: #2 finished! INFO @ Sun, 21 Jun 2020 17:45:03: #2 predicted fragment length is 81 bps INFO @ Sun, 21 Jun 2020 17:45:03: #2 alternative fragment length(s) may be 3,81 bps INFO @ Sun, 21 Jun 2020 17:45:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.20_model.r WARNING @ Sun, 21 Jun 2020 17:45:03: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:45:03: #2 You may need to consider one of the other alternative d(s): 3,81 WARNING @ Sun, 21 Jun 2020 17:45:03: #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 17:45:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:45:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:45:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:45:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:45:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.10_summits.bed INFO @ Sun, 21 Jun 2020 17:45:05: Done! pass1 - making usageList (815 chroms): 2 millis pass2 - checking and writing primary data (2344 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:45:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:45:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:45:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:45:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120693/SRX1120693.20_summits.bed INFO @ Sun, 21 Jun 2020 17:45:29: Done! pass1 - making usageList (602 chroms): 1 millis pass2 - checking and writing primary data (1502 records, 4 fields): 18 millis CompletedMACS2peakCalling