Job ID = 6458524 SRX = SRX529168 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:32:19 prefetch.2.10.7: 1) Downloading 'SRR1265774'... 2020-06-21T12:32:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:36:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:36:20 prefetch.2.10.7: 1) 'SRR1265774' was downloaded successfully Read 31914569 spots for SRR1265774/SRR1265774.sra Written 31914569 spots for SRR1265774/SRR1265774.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: 00:08:40 31914569 reads; of these: 31914569 (100.00%) were unpaired; of these: 2369685 (7.43%) aligned 0 times 20916583 (65.54%) aligned exactly 1 time 8628301 (27.04%) aligned >1 times 92.57% overall alignment rate Time searching: 00:08:40 Overall time: 00:08:40 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] 6859830 / 29544884 = 0.2322 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 21:52:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.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 21:52:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:52:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:52:32: 1000000 INFO @ Sun, 21 Jun 2020 21:52:39: 2000000 INFO @ Sun, 21 Jun 2020 21:52:45: 3000000 INFO @ Sun, 21 Jun 2020 21:52:52: 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 21:52:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.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 21:52:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:52:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:52:59: 5000000 INFO @ Sun, 21 Jun 2020 21:53:01: 1000000 INFO @ Sun, 21 Jun 2020 21:53:07: 6000000 INFO @ Sun, 21 Jun 2020 21:53:08: 2000000 INFO @ Sun, 21 Jun 2020 21:53:15: 7000000 INFO @ Sun, 21 Jun 2020 21:53:15: 3000000 INFO @ Sun, 21 Jun 2020 21:53:22: 8000000 INFO @ Sun, 21 Jun 2020 21:53:22: 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 21:53:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.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 21:53:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:53:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:53:30: 5000000 INFO @ Sun, 21 Jun 2020 21:53:30: 9000000 INFO @ Sun, 21 Jun 2020 21:53:32: 1000000 INFO @ Sun, 21 Jun 2020 21:53:37: 6000000 INFO @ Sun, 21 Jun 2020 21:53:38: 10000000 INFO @ Sun, 21 Jun 2020 21:53:40: 2000000 INFO @ Sun, 21 Jun 2020 21:53:44: 7000000 INFO @ Sun, 21 Jun 2020 21:53:46: 11000000 INFO @ Sun, 21 Jun 2020 21:53:47: 3000000 INFO @ Sun, 21 Jun 2020 21:53:51: 8000000 INFO @ Sun, 21 Jun 2020 21:53:53: 12000000 INFO @ Sun, 21 Jun 2020 21:53:55: 4000000 INFO @ Sun, 21 Jun 2020 21:53:58: 9000000 INFO @ Sun, 21 Jun 2020 21:54:01: 13000000 INFO @ Sun, 21 Jun 2020 21:54:03: 5000000 INFO @ Sun, 21 Jun 2020 21:54:05: 10000000 INFO @ Sun, 21 Jun 2020 21:54:09: 14000000 INFO @ Sun, 21 Jun 2020 21:54:10: 6000000 INFO @ Sun, 21 Jun 2020 21:54:13: 11000000 INFO @ Sun, 21 Jun 2020 21:54:16: 15000000 INFO @ Sun, 21 Jun 2020 21:54:18: 7000000 INFO @ Sun, 21 Jun 2020 21:54:20: 12000000 INFO @ Sun, 21 Jun 2020 21:54:24: 16000000 INFO @ Sun, 21 Jun 2020 21:54:25: 8000000 INFO @ Sun, 21 Jun 2020 21:54:27: 13000000 INFO @ Sun, 21 Jun 2020 21:54:32: 17000000 INFO @ Sun, 21 Jun 2020 21:54:33: 9000000 INFO @ Sun, 21 Jun 2020 21:54:34: 14000000 INFO @ Sun, 21 Jun 2020 21:54:39: 18000000 INFO @ Sun, 21 Jun 2020 21:54:41: 10000000 INFO @ Sun, 21 Jun 2020 21:54:41: 15000000 INFO @ Sun, 21 Jun 2020 21:54:47: 19000000 INFO @ Sun, 21 Jun 2020 21:54:48: 11000000 INFO @ Sun, 21 Jun 2020 21:54:49: 16000000 INFO @ Sun, 21 Jun 2020 21:54:56: 20000000 INFO @ Sun, 21 Jun 2020 21:54:56: 17000000 INFO @ Sun, 21 Jun 2020 21:54:56: 12000000 INFO @ Sun, 21 Jun 2020 21:55:03: 18000000 INFO @ Sun, 21 Jun 2020 21:55:04: 21000000 INFO @ Sun, 21 Jun 2020 21:55:04: 13000000 INFO @ Sun, 21 Jun 2020 21:55:10: 19000000 INFO @ Sun, 21 Jun 2020 21:55:11: 22000000 INFO @ Sun, 21 Jun 2020 21:55:12: 14000000 INFO @ Sun, 21 Jun 2020 21:55:17: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 21:55:17: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 21:55:17: #1 total tags in treatment: 22685054 INFO @ Sun, 21 Jun 2020 21:55:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:17: #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 21:55:18: #1 tags after filtering in treatment: 22685003 INFO @ Sun, 21 Jun 2020 21:55:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:18: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:18: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:55:18: 20000000 INFO @ Sun, 21 Jun 2020 21:55:19: #2 number of paired peaks: 388 WARNING @ Sun, 21 Jun 2020 21:55:19: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Sun, 21 Jun 2020 21:55:19: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:19: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:19: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:19: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:19: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 21:55:19: #2 alternative fragment length(s) may be 2,44,576 bps INFO @ Sun, 21 Jun 2020 21:55:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.05_model.r WARNING @ Sun, 21 Jun 2020 21:55:19: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:55:19: #2 You may need to consider one of the other alternative d(s): 2,44,576 WARNING @ Sun, 21 Jun 2020 21:55:19: #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 21:55:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:55:20: 15000000 INFO @ Sun, 21 Jun 2020 21:55:25: 21000000 INFO @ Sun, 21 Jun 2020 21:55:27: 16000000 INFO @ Sun, 21 Jun 2020 21:55:33: 22000000 INFO @ Sun, 21 Jun 2020 21:55:35: 17000000 INFO @ Sun, 21 Jun 2020 21:55:38: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 21:55:38: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 21:55:38: #1 total tags in treatment: 22685054 INFO @ Sun, 21 Jun 2020 21:55:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:38: #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 21:55:38: #1 tags after filtering in treatment: 22685003 INFO @ Sun, 21 Jun 2020 21:55:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:38: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:55:40: #2 number of paired peaks: 388 WARNING @ Sun, 21 Jun 2020 21:55:40: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Sun, 21 Jun 2020 21:55:40: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:40: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:40: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:40: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:40: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 21:55:40: #2 alternative fragment length(s) may be 2,44,576 bps INFO @ Sun, 21 Jun 2020 21:55:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.10_model.r WARNING @ Sun, 21 Jun 2020 21:55:40: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:55:40: #2 You may need to consider one of the other alternative d(s): 2,44,576 WARNING @ Sun, 21 Jun 2020 21:55:40: #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 21:55:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:55:42: 18000000 INFO @ Sun, 21 Jun 2020 21:55:48: 19000000 INFO @ Sun, 21 Jun 2020 21:55:56: 20000000 INFO @ Sun, 21 Jun 2020 21:55:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:56:02: 21000000 INFO @ Sun, 21 Jun 2020 21:56:09: 22000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:56:14: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 21:56:14: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 21:56:14: #1 total tags in treatment: 22685054 INFO @ Sun, 21 Jun 2020 21:56:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:56:14: #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 21:56:15: #1 tags after filtering in treatment: 22685003 INFO @ Sun, 21 Jun 2020 21:56:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:56:15: #1 finished! INFO @ Sun, 21 Jun 2020 21:56:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:56:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:56:16: #2 number of paired peaks: 388 WARNING @ Sun, 21 Jun 2020 21:56:16: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Sun, 21 Jun 2020 21:56:16: start model_add_line... INFO @ Sun, 21 Jun 2020 21:56:16: start X-correlation... INFO @ Sun, 21 Jun 2020 21:56:16: end of X-cor INFO @ Sun, 21 Jun 2020 21:56:16: #2 finished! INFO @ Sun, 21 Jun 2020 21:56:16: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 21:56:16: #2 alternative fragment length(s) may be 2,44,576 bps INFO @ Sun, 21 Jun 2020 21:56:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.20_model.r WARNING @ Sun, 21 Jun 2020 21:56:16: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:56:16: #2 You may need to consider one of the other alternative d(s): 2,44,576 WARNING @ Sun, 21 Jun 2020 21:56:16: #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 21:56:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:56:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:56:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:56:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:56:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.05_summits.bed INFO @ Sun, 21 Jun 2020 21:56:17: Done! pass1 - making usageList (704 chroms): 1 millis pass2 - checking and writing primary data (3959 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:56:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:56:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:56:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:56:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.10_summits.bed INFO @ Sun, 21 Jun 2020 21:56:40: Done! pass1 - making usageList (478 chroms): 1 millis pass2 - checking and writing primary data (1399 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:56:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:57:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:57:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:57:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX529168/SRX529168.20_summits.bed INFO @ Sun, 21 Jun 2020 21:57:15: Done! pass1 - making usageList (149 chroms): 1 millis pass2 - checking and writing primary data (403 records, 4 fields): 6 millis CompletedMACS2peakCalling