Job ID = 6456631 SRX = SRX385807 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:59:01 prefetch.2.10.7: 1) Downloading 'SRR1041448'... 2020-06-21T10:59:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:03:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:03:20 prefetch.2.10.7: 1) 'SRR1041448' was downloaded successfully Read 22218087 spots for SRR1041448/SRR1041448.sra Written 22218087 spots for SRR1041448/SRR1041448.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: 00:05:48 22218087 reads; of these: 22218087 (100.00%) were unpaired; of these: 1139821 (5.13%) aligned 0 times 15541253 (69.95%) aligned exactly 1 time 5537013 (24.92%) aligned >1 times 94.87% overall alignment rate Time searching: 00:05:48 Overall time: 00:05:48 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 12 files... [bam_rmdupse_core] 11025370 / 21078266 = 0.5231 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 20:14:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.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 20:14:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:14:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:14:51: 1000000 INFO @ Sun, 21 Jun 2020 20:14:58: 2000000 INFO @ Sun, 21 Jun 2020 20:15:05: 3000000 INFO @ Sun, 21 Jun 2020 20:15:12: 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 20:15:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.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 20:15:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:15:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:15:19: 5000000 INFO @ Sun, 21 Jun 2020 20:15:21: 1000000 INFO @ Sun, 21 Jun 2020 20:15:26: 6000000 INFO @ Sun, 21 Jun 2020 20:15:28: 2000000 INFO @ Sun, 21 Jun 2020 20:15:34: 7000000 INFO @ Sun, 21 Jun 2020 20:15:34: 3000000 INFO @ Sun, 21 Jun 2020 20:15:41: 4000000 INFO @ Sun, 21 Jun 2020 20:15:42: 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 20:15:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.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 20:15:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:15:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:15:48: 5000000 INFO @ Sun, 21 Jun 2020 20:15:50: 9000000 INFO @ Sun, 21 Jun 2020 20:15:51: 1000000 INFO @ Sun, 21 Jun 2020 20:15:55: 6000000 INFO @ Sun, 21 Jun 2020 20:15:58: 10000000 INFO @ Sun, 21 Jun 2020 20:15:58: 2000000 INFO @ Sun, 21 Jun 2020 20:15:58: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:15:58: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:15:58: #1 total tags in treatment: 10052896 INFO @ Sun, 21 Jun 2020 20:15:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:15:58: #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 20:15:58: #1 tags after filtering in treatment: 10052825 INFO @ Sun, 21 Jun 2020 20:15:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:15:58: #1 finished! INFO @ Sun, 21 Jun 2020 20:15:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:15:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:15:59: #2 number of paired peaks: 1718 INFO @ Sun, 21 Jun 2020 20:15:59: start model_add_line... INFO @ Sun, 21 Jun 2020 20:15:59: start X-correlation... INFO @ Sun, 21 Jun 2020 20:15:59: end of X-cor INFO @ Sun, 21 Jun 2020 20:15:59: #2 finished! INFO @ Sun, 21 Jun 2020 20:15:59: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 20:15:59: #2 alternative fragment length(s) may be 4,76 bps INFO @ Sun, 21 Jun 2020 20:15:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.05_model.r WARNING @ Sun, 21 Jun 2020 20:15:59: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:15:59: #2 You may need to consider one of the other alternative d(s): 4,76 WARNING @ Sun, 21 Jun 2020 20:15:59: #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 20:15:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:15:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:16:01: 7000000 INFO @ Sun, 21 Jun 2020 20:16:04: 3000000 INFO @ Sun, 21 Jun 2020 20:16:08: 8000000 INFO @ Sun, 21 Jun 2020 20:16:11: 4000000 INFO @ Sun, 21 Jun 2020 20:16:15: 9000000 INFO @ Sun, 21 Jun 2020 20:16:18: 5000000 INFO @ Sun, 21 Jun 2020 20:16:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:16:21: 10000000 INFO @ Sun, 21 Jun 2020 20:16:22: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:16:22: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:16:22: #1 total tags in treatment: 10052896 INFO @ Sun, 21 Jun 2020 20:16:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:16:22: #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 20:16:22: #1 tags after filtering in treatment: 10052825 INFO @ Sun, 21 Jun 2020 20:16:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:16:22: #1 finished! INFO @ Sun, 21 Jun 2020 20:16:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:16:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:16:23: #2 number of paired peaks: 1718 INFO @ Sun, 21 Jun 2020 20:16:23: start model_add_line... INFO @ Sun, 21 Jun 2020 20:16:23: start X-correlation... INFO @ Sun, 21 Jun 2020 20:16:23: end of X-cor INFO @ Sun, 21 Jun 2020 20:16:23: #2 finished! INFO @ Sun, 21 Jun 2020 20:16:23: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 20:16:23: #2 alternative fragment length(s) may be 4,76 bps INFO @ Sun, 21 Jun 2020 20:16:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.10_model.r WARNING @ Sun, 21 Jun 2020 20:16:23: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:16:23: #2 You may need to consider one of the other alternative d(s): 4,76 WARNING @ Sun, 21 Jun 2020 20:16:23: #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 20:16:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:16:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:16:24: 6000000 INFO @ Sun, 21 Jun 2020 20:16:30: 7000000 INFO @ Sun, 21 Jun 2020 20:16:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:16:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:16:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.05_summits.bed INFO @ Sun, 21 Jun 2020 20:16:32: Done! pass1 - making usageList (828 chroms): 2 millis pass2 - checking and writing primary data (5446 records, 4 fields): 25 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:16:36: 8000000 INFO @ Sun, 21 Jun 2020 20:16:42: 9000000 INFO @ Sun, 21 Jun 2020 20:16:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:16:47: 10000000 INFO @ Sun, 21 Jun 2020 20:16:48: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:16:48: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:16:48: #1 total tags in treatment: 10052896 INFO @ Sun, 21 Jun 2020 20:16:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:16:48: #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 20:16:48: #1 tags after filtering in treatment: 10052825 INFO @ Sun, 21 Jun 2020 20:16:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:16:48: #1 finished! INFO @ Sun, 21 Jun 2020 20:16:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:16:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:16:49: #2 number of paired peaks: 1718 INFO @ Sun, 21 Jun 2020 20:16:49: start model_add_line... INFO @ Sun, 21 Jun 2020 20:16:49: start X-correlation... INFO @ Sun, 21 Jun 2020 20:16:49: end of X-cor INFO @ Sun, 21 Jun 2020 20:16:49: #2 finished! INFO @ Sun, 21 Jun 2020 20:16:49: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 20:16:49: #2 alternative fragment length(s) may be 4,76 bps INFO @ Sun, 21 Jun 2020 20:16:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.20_model.r WARNING @ Sun, 21 Jun 2020 20:16:49: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:16:49: #2 You may need to consider one of the other alternative d(s): 4,76 WARNING @ Sun, 21 Jun 2020 20:16:49: #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 20:16:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:16:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:16:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:16:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:16:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.10_summits.bed INFO @ Sun, 21 Jun 2020 20:16:54: Done! pass1 - making usageList (675 chroms): 1 millis pass2 - checking and writing primary data (3001 records, 4 fields): 20 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:17:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:17:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:17:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:17:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX385807/SRX385807.20_summits.bed INFO @ Sun, 21 Jun 2020 20:17:21: Done! pass1 - making usageList (418 chroms): 1 millis pass2 - checking and writing primary data (1127 records, 4 fields): 13 millis CompletedMACS2peakCalling