Job ID = 6498304 SRX = SRX467115 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:26:16 prefetch.2.10.7: 1) Downloading 'SRR1164539'... 2020-06-25T23:26:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:27:49 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:27:50 prefetch.2.10.7: 'SRR1164539' is valid 2020-06-25T23:27:50 prefetch.2.10.7: 1) 'SRR1164539' was downloaded successfully Read 13532491 spots for SRR1164539/SRR1164539.sra Written 13532491 spots for SRR1164539/SRR1164539.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: 00:05:39 13532491 reads; of these: 13532491 (100.00%) were unpaired; of these: 796496 (5.89%) aligned 0 times 7785958 (57.54%) aligned exactly 1 time 4950037 (36.58%) aligned >1 times 94.11% overall alignment rate Time searching: 00:05:39 Overall time: 00:05:39 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 8 files... [bam_rmdupse_core] 1488511 / 12735995 = 0.1169 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 08:38:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.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 08:38:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:38:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:38:15: 1000000 INFO @ Fri, 26 Jun 2020 08:38:20: 2000000 INFO @ Fri, 26 Jun 2020 08:38:26: 3000000 INFO @ Fri, 26 Jun 2020 08:38:31: 4000000 INFO @ Fri, 26 Jun 2020 08:38:36: 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 @ Fri, 26 Jun 2020 08:38:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.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 08:38:39: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:38:39: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:38:42: 6000000 INFO @ Fri, 26 Jun 2020 08:38:45: 1000000 INFO @ Fri, 26 Jun 2020 08:38:47: 7000000 INFO @ Fri, 26 Jun 2020 08:38:50: 2000000 INFO @ Fri, 26 Jun 2020 08:38:52: 8000000 INFO @ Fri, 26 Jun 2020 08:38:56: 3000000 INFO @ Fri, 26 Jun 2020 08:38:58: 9000000 INFO @ Fri, 26 Jun 2020 08:39:01: 4000000 INFO @ Fri, 26 Jun 2020 08:39:03: 10000000 INFO @ Fri, 26 Jun 2020 08:39:07: 5000000 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 08:39:09: 11000000 INFO @ Fri, 26 Jun 2020 08:39:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.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 08:39:09: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:39:09: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:39:10: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:39:10: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:39:10: #1 total tags in treatment: 11247484 INFO @ Fri, 26 Jun 2020 08:39:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:39:10: #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 08:39:10: #1 tags after filtering in treatment: 11247484 INFO @ Fri, 26 Jun 2020 08:39:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:39:10: #1 finished! INFO @ Fri, 26 Jun 2020 08:39:10: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:39:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:39:11: #2 number of paired peaks: 1130 INFO @ Fri, 26 Jun 2020 08:39:11: start model_add_line... INFO @ Fri, 26 Jun 2020 08:39:11: start X-correlation... INFO @ Fri, 26 Jun 2020 08:39:11: end of X-cor INFO @ Fri, 26 Jun 2020 08:39:11: #2 finished! INFO @ Fri, 26 Jun 2020 08:39:11: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 08:39:11: #2 alternative fragment length(s) may be 4,49,536 bps INFO @ Fri, 26 Jun 2020 08:39:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.05_model.r WARNING @ Fri, 26 Jun 2020 08:39:11: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:39:11: #2 You may need to consider one of the other alternative d(s): 4,49,536 WARNING @ Fri, 26 Jun 2020 08:39:11: #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 08:39:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:39:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:39:12: 6000000 INFO @ Fri, 26 Jun 2020 08:39:15: 1000000 INFO @ Fri, 26 Jun 2020 08:39:18: 7000000 INFO @ Fri, 26 Jun 2020 08:39:21: 2000000 INFO @ Fri, 26 Jun 2020 08:39:23: 8000000 INFO @ Fri, 26 Jun 2020 08:39:26: 3000000 INFO @ Fri, 26 Jun 2020 08:39:28: 9000000 INFO @ Fri, 26 Jun 2020 08:39:32: 4000000 INFO @ Fri, 26 Jun 2020 08:39:34: 10000000 INFO @ Fri, 26 Jun 2020 08:39:36: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:39:37: 5000000 INFO @ Fri, 26 Jun 2020 08:39:39: 11000000 INFO @ Fri, 26 Jun 2020 08:39:40: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:39:40: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:39:40: #1 total tags in treatment: 11247484 INFO @ Fri, 26 Jun 2020 08:39:40: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:39:40: #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 08:39:41: #1 tags after filtering in treatment: 11247484 INFO @ Fri, 26 Jun 2020 08:39:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:39:41: #1 finished! INFO @ Fri, 26 Jun 2020 08:39:41: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:39:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:39:41: #2 number of paired peaks: 1130 INFO @ Fri, 26 Jun 2020 08:39:41: start model_add_line... INFO @ Fri, 26 Jun 2020 08:39:42: start X-correlation... INFO @ Fri, 26 Jun 2020 08:39:42: end of X-cor INFO @ Fri, 26 Jun 2020 08:39:42: #2 finished! INFO @ Fri, 26 Jun 2020 08:39:42: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 08:39:42: #2 alternative fragment length(s) may be 4,49,536 bps INFO @ Fri, 26 Jun 2020 08:39:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.10_model.r WARNING @ Fri, 26 Jun 2020 08:39:42: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:39:42: #2 You may need to consider one of the other alternative d(s): 4,49,536 WARNING @ Fri, 26 Jun 2020 08:39:42: #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 08:39:42: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:39:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:39:42: 6000000 INFO @ Fri, 26 Jun 2020 08:39:48: 7000000 INFO @ Fri, 26 Jun 2020 08:39:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:39:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:39:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.05_summits.bed INFO @ Fri, 26 Jun 2020 08:39:48: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3516 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:39:53: 8000000 INFO @ Fri, 26 Jun 2020 08:39:58: 9000000 INFO @ Fri, 26 Jun 2020 08:40:03: 10000000 INFO @ Fri, 26 Jun 2020 08:40:06: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:40:09: 11000000 INFO @ Fri, 26 Jun 2020 08:40:10: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:40:10: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:40:10: #1 total tags in treatment: 11247484 INFO @ Fri, 26 Jun 2020 08:40:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:40:10: #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 08:40:10: #1 tags after filtering in treatment: 11247484 INFO @ Fri, 26 Jun 2020 08:40:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:40:10: #1 finished! INFO @ Fri, 26 Jun 2020 08:40:10: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:40:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:40:11: #2 number of paired peaks: 1130 INFO @ Fri, 26 Jun 2020 08:40:11: start model_add_line... INFO @ Fri, 26 Jun 2020 08:40:11: start X-correlation... INFO @ Fri, 26 Jun 2020 08:40:11: end of X-cor INFO @ Fri, 26 Jun 2020 08:40:11: #2 finished! INFO @ Fri, 26 Jun 2020 08:40:11: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 08:40:11: #2 alternative fragment length(s) may be 4,49,536 bps INFO @ Fri, 26 Jun 2020 08:40:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.20_model.r WARNING @ Fri, 26 Jun 2020 08:40:11: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:40:11: #2 You may need to consider one of the other alternative d(s): 4,49,536 WARNING @ Fri, 26 Jun 2020 08:40:11: #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 08:40:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:40:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:40:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:40:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:40:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.10_summits.bed INFO @ Fri, 26 Jun 2020 08:40:18: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2395 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:40:36: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:40:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:40:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:40:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467115/SRX467115.20_summits.bed INFO @ Fri, 26 Jun 2020 08:40:48: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1007 records, 4 fields): 3 millis CompletedMACS2peakCalling