Job ID = 6458297 SRX = SRX5011053 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:31:07 prefetch.2.10.7: 1) Downloading 'SRR8191502'... 2020-06-21T12:31:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:32:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:32:44 prefetch.2.10.7: 'SRR8191502' is valid 2020-06-21T12:32:44 prefetch.2.10.7: 1) 'SRR8191502' was downloaded successfully 2020-06-21T12:32:44 prefetch.2.10.7: 'SRR8191502' has 0 unresolved dependencies Read 25449790 spots for SRR8191502/SRR8191502.sra Written 25449790 spots for SRR8191502/SRR8191502.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: 00:07:15 25449790 reads; of these: 25449790 (100.00%) were unpaired; of these: 2290569 (9.00%) aligned 0 times 16717253 (65.69%) aligned exactly 1 time 6441968 (25.31%) aligned >1 times 91.00% overall alignment rate Time searching: 00:07:15 Overall time: 00:07:15 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] 11734844 / 23159221 = 0.5067 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 21:45:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.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 21:45:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:45:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:45:18: 1000000 INFO @ Sun, 21 Jun 2020 21:45:25: 2000000 INFO @ Sun, 21 Jun 2020 21:45:32: 3000000 INFO @ Sun, 21 Jun 2020 21:45:39: 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 21:45:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.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 21:45:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:45:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:45:46: 5000000 INFO @ Sun, 21 Jun 2020 21:45:48: 1000000 INFO @ Sun, 21 Jun 2020 21:45:54: 6000000 INFO @ Sun, 21 Jun 2020 21:45:55: 2000000 INFO @ Sun, 21 Jun 2020 21:46:01: 7000000 INFO @ Sun, 21 Jun 2020 21:46:02: 3000000 INFO @ Sun, 21 Jun 2020 21:46:08: 8000000 INFO @ Sun, 21 Jun 2020 21:46:09: 4000000 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 21:46:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.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 21:46:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:46:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:46:15: 5000000 INFO @ Sun, 21 Jun 2020 21:46:16: 9000000 INFO @ Sun, 21 Jun 2020 21:46:18: 1000000 INFO @ Sun, 21 Jun 2020 21:46:22: 6000000 INFO @ Sun, 21 Jun 2020 21:46:23: 10000000 INFO @ Sun, 21 Jun 2020 21:46:25: 2000000 INFO @ Sun, 21 Jun 2020 21:46:29: 7000000 INFO @ Sun, 21 Jun 2020 21:46:30: 11000000 INFO @ Sun, 21 Jun 2020 21:46:32: 3000000 INFO @ Sun, 21 Jun 2020 21:46:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:46:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:46:33: #1 total tags in treatment: 11424377 INFO @ Sun, 21 Jun 2020 21:46:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:46:33: #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 21:46:34: #1 tags after filtering in treatment: 11424310 INFO @ Sun, 21 Jun 2020 21:46:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:46:34: #1 finished! INFO @ Sun, 21 Jun 2020 21:46:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:46:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:46:35: #2 number of paired peaks: 1797 INFO @ Sun, 21 Jun 2020 21:46:35: start model_add_line... INFO @ Sun, 21 Jun 2020 21:46:35: start X-correlation... INFO @ Sun, 21 Jun 2020 21:46:35: end of X-cor INFO @ Sun, 21 Jun 2020 21:46:35: #2 finished! INFO @ Sun, 21 Jun 2020 21:46:35: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 21:46:35: #2 alternative fragment length(s) may be 3,54 bps INFO @ Sun, 21 Jun 2020 21:46:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.05_model.r WARNING @ Sun, 21 Jun 2020 21:46:35: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:46:35: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Sun, 21 Jun 2020 21:46:35: #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 21:46:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:46:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:46:35: 8000000 INFO @ Sun, 21 Jun 2020 21:46:38: 4000000 INFO @ Sun, 21 Jun 2020 21:46:42: 9000000 INFO @ Sun, 21 Jun 2020 21:46:45: 5000000 INFO @ Sun, 21 Jun 2020 21:46:48: 10000000 INFO @ Sun, 21 Jun 2020 21:46:51: 6000000 INFO @ Sun, 21 Jun 2020 21:46:54: 11000000 INFO @ Sun, 21 Jun 2020 21:46:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:46:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:46:57: #1 total tags in treatment: 11424377 INFO @ Sun, 21 Jun 2020 21:46:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:46:57: #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 21:46:57: 7000000 INFO @ Sun, 21 Jun 2020 21:46:57: #1 tags after filtering in treatment: 11424310 INFO @ Sun, 21 Jun 2020 21:46:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:46:57: #1 finished! INFO @ Sun, 21 Jun 2020 21:46:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:46:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:46:58: #2 number of paired peaks: 1797 INFO @ Sun, 21 Jun 2020 21:46:58: start model_add_line... INFO @ Sun, 21 Jun 2020 21:46:59: start X-correlation... INFO @ Sun, 21 Jun 2020 21:46:59: end of X-cor INFO @ Sun, 21 Jun 2020 21:46:59: #2 finished! INFO @ Sun, 21 Jun 2020 21:46:59: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 21:46:59: #2 alternative fragment length(s) may be 3,54 bps INFO @ Sun, 21 Jun 2020 21:46:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.10_model.r WARNING @ Sun, 21 Jun 2020 21:46:59: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:46:59: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Sun, 21 Jun 2020 21:46:59: #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 21:46:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:46:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:47:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:47:03: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:47:09: 9000000 INFO @ Sun, 21 Jun 2020 21:47:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:47:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:47:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.05_summits.bed INFO @ Sun, 21 Jun 2020 21:47:13: Done! pass1 - making usageList (762 chroms): 2 millis pass2 - checking and writing primary data (3935 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:47:15: 10000000 INFO @ Sun, 21 Jun 2020 21:47:20: 11000000 INFO @ Sun, 21 Jun 2020 21:47:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:47:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:47:23: #1 total tags in treatment: 11424377 INFO @ Sun, 21 Jun 2020 21:47:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:47:23: #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 21:47:23: #1 tags after filtering in treatment: 11424310 INFO @ Sun, 21 Jun 2020 21:47:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:47:23: #1 finished! INFO @ Sun, 21 Jun 2020 21:47:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:47:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:47:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:47:24: #2 number of paired peaks: 1797 INFO @ Sun, 21 Jun 2020 21:47:24: start model_add_line... INFO @ Sun, 21 Jun 2020 21:47:24: start X-correlation... INFO @ Sun, 21 Jun 2020 21:47:24: end of X-cor INFO @ Sun, 21 Jun 2020 21:47:24: #2 finished! INFO @ Sun, 21 Jun 2020 21:47:24: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 21:47:24: #2 alternative fragment length(s) may be 3,54 bps INFO @ Sun, 21 Jun 2020 21:47:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.20_model.r WARNING @ Sun, 21 Jun 2020 21:47:24: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:47:24: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Sun, 21 Jun 2020 21:47:24: #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 21:47:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:47:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:47:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:47:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:47:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.10_summits.bed INFO @ Sun, 21 Jun 2020 21:47:35: Done! pass1 - making usageList (625 chroms): 1 millis pass2 - checking and writing primary data (2351 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:47:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:48:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:48:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:48:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011053/SRX5011053.20_summits.bed INFO @ Sun, 21 Jun 2020 21:48:02: Done! pass1 - making usageList (324 chroms): 1 millis pass2 - checking and writing primary data (747 records, 4 fields): 12 millis CompletedMACS2peakCalling