Job ID = 6455626 SRX = SRX287938 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:07:51 prefetch.2.10.7: 1) Downloading 'SRR870127'... 2020-06-21T10:07:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:13:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:13:42 prefetch.2.10.7: 1) 'SRR870127' was downloaded successfully Read 21425213 spots for SRR870127/SRR870127.sra Written 21425213 spots for SRR870127/SRR870127.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: 00:08:44 21425213 reads; of these: 21425213 (100.00%) were unpaired; of these: 5522128 (25.77%) aligned 0 times 5814792 (27.14%) aligned exactly 1 time 10088293 (47.09%) aligned >1 times 74.23% overall alignment rate Time searching: 00:08:44 Overall time: 00:08:44 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] 9158254 / 15903085 = 0.5759 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 19:27:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.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 19:27:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:27:10: 1000000 INFO @ Sun, 21 Jun 2020 19:27:18: 2000000 INFO @ Sun, 21 Jun 2020 19:27:26: 3000000 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 19:27:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.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 19:27:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:27:33: 4000000 INFO @ Sun, 21 Jun 2020 19:27:40: 1000000 INFO @ Sun, 21 Jun 2020 19:27:42: 5000000 INFO @ Sun, 21 Jun 2020 19:27:48: 2000000 INFO @ Sun, 21 Jun 2020 19:27:51: 6000000 INFO @ Sun, 21 Jun 2020 19:27:56: 3000000 INFO @ Sun, 21 Jun 2020 19:27:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:27:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:27:58: #1 total tags in treatment: 6744831 INFO @ Sun, 21 Jun 2020 19:27:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:27:58: #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 19:27:58: #1 tags after filtering in treatment: 6744827 INFO @ Sun, 21 Jun 2020 19:27:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:27:58: #1 finished! INFO @ Sun, 21 Jun 2020 19:27:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:27:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:27:59: #2 number of paired peaks: 1536 INFO @ Sun, 21 Jun 2020 19:27:59: start model_add_line... INFO @ Sun, 21 Jun 2020 19:27:59: start X-correlation... INFO @ Sun, 21 Jun 2020 19:27:59: end of X-cor INFO @ Sun, 21 Jun 2020 19:27:59: #2 finished! INFO @ Sun, 21 Jun 2020 19:27:59: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 19:27:59: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sun, 21 Jun 2020 19:27:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.05_model.r WARNING @ Sun, 21 Jun 2020 19:27:59: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:27:59: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sun, 21 Jun 2020 19:27:59: #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 19:27:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:27:59: #3 Pre-compute pvalue-qvalue table... 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 19:28:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.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 19:28:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:28:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:28:03: 4000000 INFO @ Sun, 21 Jun 2020 19:28:10: 1000000 INFO @ Sun, 21 Jun 2020 19:28:11: 5000000 INFO @ Sun, 21 Jun 2020 19:28:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:28:18: 2000000 INFO @ Sun, 21 Jun 2020 19:28:19: 6000000 INFO @ Sun, 21 Jun 2020 19:28:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:28:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:28:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.05_summits.bed INFO @ Sun, 21 Jun 2020 19:28:22: Done! pass1 - making usageList (749 chroms): 1 millis pass2 - checking and writing primary data (3027 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:28:25: 3000000 INFO @ Sun, 21 Jun 2020 19:28:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:28:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:28:25: #1 total tags in treatment: 6744831 INFO @ Sun, 21 Jun 2020 19:28:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:28:25: #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 19:28:26: #1 tags after filtering in treatment: 6744827 INFO @ Sun, 21 Jun 2020 19:28:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:28:26: #1 finished! INFO @ Sun, 21 Jun 2020 19:28:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:28:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:28:26: #2 number of paired peaks: 1536 INFO @ Sun, 21 Jun 2020 19:28:26: start model_add_line... INFO @ Sun, 21 Jun 2020 19:28:27: start X-correlation... INFO @ Sun, 21 Jun 2020 19:28:27: end of X-cor INFO @ Sun, 21 Jun 2020 19:28:27: #2 finished! INFO @ Sun, 21 Jun 2020 19:28:27: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 19:28:27: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sun, 21 Jun 2020 19:28:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.10_model.r WARNING @ Sun, 21 Jun 2020 19:28:27: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:28:27: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sun, 21 Jun 2020 19:28:27: #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 19:28:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:28:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:28:32: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:28:40: 5000000 INFO @ Sun, 21 Jun 2020 19:28:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:28:47: 6000000 INFO @ Sun, 21 Jun 2020 19:28:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:28:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:28:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.10_summits.bed INFO @ Sun, 21 Jun 2020 19:28:51: Done! pass1 - making usageList (583 chroms): 1 millis pass2 - checking and writing primary data (2179 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:28:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:28:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:28:52: #1 total tags in treatment: 6744831 INFO @ Sun, 21 Jun 2020 19:28:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:28:52: #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 19:28:52: #1 tags after filtering in treatment: 6744827 INFO @ Sun, 21 Jun 2020 19:28:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:28:52: #1 finished! INFO @ Sun, 21 Jun 2020 19:28:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:28:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:28:53: #2 number of paired peaks: 1536 INFO @ Sun, 21 Jun 2020 19:28:53: start model_add_line... INFO @ Sun, 21 Jun 2020 19:28:53: start X-correlation... INFO @ Sun, 21 Jun 2020 19:28:53: end of X-cor INFO @ Sun, 21 Jun 2020 19:28:53: #2 finished! INFO @ Sun, 21 Jun 2020 19:28:53: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 19:28:53: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sun, 21 Jun 2020 19:28:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.20_model.r WARNING @ Sun, 21 Jun 2020 19:28:53: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:28:53: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sun, 21 Jun 2020 19:28:53: #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 19:28:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:28:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:29:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:29:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:29:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:29:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287938/SRX287938.20_summits.bed INFO @ Sun, 21 Jun 2020 19:29:16: Done! pass1 - making usageList (461 chroms): 1 millis pass2 - checking and writing primary data (1345 records, 4 fields): 16 millis CompletedMACS2peakCalling