Job ID = 6458300 SRX = SRX5011056 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:17:52 prefetch.2.10.7: 1) Downloading 'SRR8191505'... 2020-06-21T12:17:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:20:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:20:30 prefetch.2.10.7: 'SRR8191505' is valid 2020-06-21T12:20:30 prefetch.2.10.7: 1) 'SRR8191505' was downloaded successfully 2020-06-21T12:20:30 prefetch.2.10.7: 'SRR8191505' has 0 unresolved dependencies Read 32830552 spots for SRR8191505/SRR8191505.sra Written 32830552 spots for SRR8191505/SRR8191505.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: 00:08:49 32830552 reads; of these: 32830552 (100.00%) were unpaired; of these: 2880038 (8.77%) aligned 0 times 21437472 (65.30%) aligned exactly 1 time 8513042 (25.93%) aligned >1 times 91.23% overall alignment rate Time searching: 00:08:49 Overall time: 00:08:49 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 16 files... [bam_rmdupse_core] 16049853 / 29950514 = 0.5359 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 21:35:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.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 21:35:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:35:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:35:25: 1000000 INFO @ Sun, 21 Jun 2020 21:35:31: 2000000 INFO @ Sun, 21 Jun 2020 21:35:37: 3000000 INFO @ Sun, 21 Jun 2020 21:35:42: 4000000 INFO @ Sun, 21 Jun 2020 21:35:48: 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 @ Sun, 21 Jun 2020 21:35:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.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 21:35:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:35:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:35:54: 6000000 INFO @ Sun, 21 Jun 2020 21:35:57: 1000000 INFO @ Sun, 21 Jun 2020 21:36:00: 7000000 INFO @ Sun, 21 Jun 2020 21:36:04: 2000000 INFO @ Sun, 21 Jun 2020 21:36:07: 8000000 INFO @ Sun, 21 Jun 2020 21:36:12: 3000000 INFO @ Sun, 21 Jun 2020 21:36:13: 9000000 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 21:36:19: 4000000 INFO @ Sun, 21 Jun 2020 21:36:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.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 21:36:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:36:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:36:20: 10000000 INFO @ Sun, 21 Jun 2020 21:36:26: 5000000 INFO @ Sun, 21 Jun 2020 21:36:27: 1000000 INFO @ Sun, 21 Jun 2020 21:36:27: 11000000 INFO @ Sun, 21 Jun 2020 21:36:33: 6000000 INFO @ Sun, 21 Jun 2020 21:36:33: 2000000 INFO @ Sun, 21 Jun 2020 21:36:34: 12000000 INFO @ Sun, 21 Jun 2020 21:36:40: 3000000 INFO @ Sun, 21 Jun 2020 21:36:41: 7000000 INFO @ Sun, 21 Jun 2020 21:36:41: 13000000 INFO @ Sun, 21 Jun 2020 21:36:47: 4000000 INFO @ Sun, 21 Jun 2020 21:36:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:36:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:36:47: #1 total tags in treatment: 13900661 INFO @ Sun, 21 Jun 2020 21:36:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:36:47: #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 21:36:47: #1 tags after filtering in treatment: 13900606 INFO @ Sun, 21 Jun 2020 21:36:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:36:47: #1 finished! INFO @ Sun, 21 Jun 2020 21:36:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:36:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:36:48: 8000000 INFO @ Sun, 21 Jun 2020 21:36:48: #2 number of paired peaks: 2028 INFO @ Sun, 21 Jun 2020 21:36:48: start model_add_line... INFO @ Sun, 21 Jun 2020 21:36:49: start X-correlation... INFO @ Sun, 21 Jun 2020 21:36:49: end of X-cor INFO @ Sun, 21 Jun 2020 21:36:49: #2 finished! INFO @ Sun, 21 Jun 2020 21:36:49: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 21:36:49: #2 alternative fragment length(s) may be 2,53 bps INFO @ Sun, 21 Jun 2020 21:36:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.05_model.r WARNING @ Sun, 21 Jun 2020 21:36:49: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:36:49: #2 You may need to consider one of the other alternative d(s): 2,53 WARNING @ Sun, 21 Jun 2020 21:36:49: #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 21:36:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:36:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:36:53: 5000000 INFO @ Sun, 21 Jun 2020 21:36:56: 9000000 INFO @ Sun, 21 Jun 2020 21:37:00: 6000000 INFO @ Sun, 21 Jun 2020 21:37:03: 10000000 INFO @ Sun, 21 Jun 2020 21:37:06: 7000000 INFO @ Sun, 21 Jun 2020 21:37:11: 11000000 INFO @ Sun, 21 Jun 2020 21:37:13: 8000000 INFO @ Sun, 21 Jun 2020 21:37:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:37:18: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:37:19: 9000000 INFO @ Sun, 21 Jun 2020 21:37:26: 13000000 INFO @ Sun, 21 Jun 2020 21:37:26: 10000000 INFO @ Sun, 21 Jun 2020 21:37:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:37:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:37:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.05_summits.bed INFO @ Sun, 21 Jun 2020 21:37:29: Done! pass1 - making usageList (789 chroms): 1 millis pass2 - checking and writing primary data (4349 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:37:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:37:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:37:32: #1 total tags in treatment: 13900661 INFO @ Sun, 21 Jun 2020 21:37:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:37:32: #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 21:37:33: #1 tags after filtering in treatment: 13900606 INFO @ Sun, 21 Jun 2020 21:37:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:37:33: #1 finished! INFO @ Sun, 21 Jun 2020 21:37:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:37:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:37:33: 11000000 INFO @ Sun, 21 Jun 2020 21:37:34: #2 number of paired peaks: 2028 INFO @ Sun, 21 Jun 2020 21:37:34: start model_add_line... INFO @ Sun, 21 Jun 2020 21:37:34: start X-correlation... INFO @ Sun, 21 Jun 2020 21:37:34: end of X-cor INFO @ Sun, 21 Jun 2020 21:37:34: #2 finished! INFO @ Sun, 21 Jun 2020 21:37:34: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 21:37:34: #2 alternative fragment length(s) may be 2,53 bps INFO @ Sun, 21 Jun 2020 21:37:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.10_model.r WARNING @ Sun, 21 Jun 2020 21:37:34: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:37:34: #2 You may need to consider one of the other alternative d(s): 2,53 WARNING @ Sun, 21 Jun 2020 21:37:34: #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 21:37:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:37:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:37:39: 12000000 INFO @ Sun, 21 Jun 2020 21:37:45: 13000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:37:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:37:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:37:51: #1 total tags in treatment: 13900661 INFO @ Sun, 21 Jun 2020 21:37:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:37:51: #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 21:37:51: #1 tags after filtering in treatment: 13900606 INFO @ Sun, 21 Jun 2020 21:37:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:37:51: #1 finished! INFO @ Sun, 21 Jun 2020 21:37:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:37:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:37:52: #2 number of paired peaks: 2028 INFO @ Sun, 21 Jun 2020 21:37:52: start model_add_line... INFO @ Sun, 21 Jun 2020 21:37:52: start X-correlation... INFO @ Sun, 21 Jun 2020 21:37:52: end of X-cor INFO @ Sun, 21 Jun 2020 21:37:52: #2 finished! INFO @ Sun, 21 Jun 2020 21:37:52: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 21:37:52: #2 alternative fragment length(s) may be 2,53 bps INFO @ Sun, 21 Jun 2020 21:37:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.20_model.r WARNING @ Sun, 21 Jun 2020 21:37:52: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:37:52: #2 You may need to consider one of the other alternative d(s): 2,53 WARNING @ Sun, 21 Jun 2020 21:37:52: #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 21:37:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:37:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:38:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:38:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:38:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:38:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.10_summits.bed INFO @ Sun, 21 Jun 2020 21:38:14: Done! pass1 - making usageList (685 chroms): 1 millis pass2 - checking and writing primary data (2909 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:38:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:38:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:38:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:38:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011056/SRX5011056.20_summits.bed INFO @ Sun, 21 Jun 2020 21:38:33: Done! pass1 - making usageList (455 chroms): 1 millis pass2 - checking and writing primary data (1139 records, 4 fields): 14 millis CompletedMACS2peakCalling