Job ID = 6528120 SRX = SRX467060 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:33:06 prefetch.2.10.7: 1) Downloading 'SRR1164484'... 2020-06-29T14:33:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:37:48 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:37:48 prefetch.2.10.7: 1) 'SRR1164484' was downloaded successfully Read 29119791 spots for SRR1164484/SRR1164484.sra Written 29119791 spots for SRR1164484/SRR1164484.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: 00:21:44 29119791 reads; of these: 29119791 (100.00%) were unpaired; of these: 972518 (3.34%) aligned 0 times 10972390 (37.68%) aligned exactly 1 time 17174883 (58.98%) aligned >1 times 96.66% overall alignment rate Time searching: 00:21:44 Overall time: 00:21:44 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 11589211 / 28147273 = 0.4117 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 @ Tue, 30 Jun 2020 00:12:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.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 @ Tue, 30 Jun 2020 00:12:31: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:12:31: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:12:38: 1000000 INFO @ Tue, 30 Jun 2020 00:12:44: 2000000 INFO @ Tue, 30 Jun 2020 00:12:51: 3000000 INFO @ Tue, 30 Jun 2020 00:12:57: 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 @ Tue, 30 Jun 2020 00:13:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.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 @ Tue, 30 Jun 2020 00:13:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:13:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:13:03: 5000000 INFO @ Tue, 30 Jun 2020 00:13:08: 1000000 INFO @ Tue, 30 Jun 2020 00:13:10: 6000000 INFO @ Tue, 30 Jun 2020 00:13:14: 2000000 INFO @ Tue, 30 Jun 2020 00:13:16: 7000000 INFO @ Tue, 30 Jun 2020 00:13:21: 3000000 INFO @ Tue, 30 Jun 2020 00:13:22: 8000000 INFO @ Tue, 30 Jun 2020 00:13:27: 4000000 INFO @ Tue, 30 Jun 2020 00:13:29: 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 @ Tue, 30 Jun 2020 00:13:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.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 @ Tue, 30 Jun 2020 00:13:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:13:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:13:34: 5000000 INFO @ Tue, 30 Jun 2020 00:13:35: 10000000 INFO @ Tue, 30 Jun 2020 00:13:38: 1000000 INFO @ Tue, 30 Jun 2020 00:13:40: 6000000 INFO @ Tue, 30 Jun 2020 00:13:42: 11000000 INFO @ Tue, 30 Jun 2020 00:13:45: 2000000 INFO @ Tue, 30 Jun 2020 00:13:47: 7000000 INFO @ Tue, 30 Jun 2020 00:13:49: 12000000 INFO @ Tue, 30 Jun 2020 00:13:52: 3000000 INFO @ Tue, 30 Jun 2020 00:13:54: 8000000 INFO @ Tue, 30 Jun 2020 00:13:56: 13000000 INFO @ Tue, 30 Jun 2020 00:13:59: 4000000 INFO @ Tue, 30 Jun 2020 00:14:01: 9000000 INFO @ Tue, 30 Jun 2020 00:14:03: 14000000 INFO @ Tue, 30 Jun 2020 00:14:06: 5000000 INFO @ Tue, 30 Jun 2020 00:14:08: 10000000 INFO @ Tue, 30 Jun 2020 00:14:09: 15000000 INFO @ Tue, 30 Jun 2020 00:14:12: 6000000 INFO @ Tue, 30 Jun 2020 00:14:15: 11000000 INFO @ Tue, 30 Jun 2020 00:14:16: 16000000 INFO @ Tue, 30 Jun 2020 00:14:19: 7000000 INFO @ Tue, 30 Jun 2020 00:14:20: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:14:20: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:14:20: #1 total tags in treatment: 16558062 INFO @ Tue, 30 Jun 2020 00:14:20: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:14:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:14:20: #1 tags after filtering in treatment: 16558062 INFO @ Tue, 30 Jun 2020 00:14:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:14:20: #1 finished! INFO @ Tue, 30 Jun 2020 00:14:20: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:14:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:14:21: #2 number of paired peaks: 140 WARNING @ Tue, 30 Jun 2020 00:14:21: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 30 Jun 2020 00:14:21: start model_add_line... INFO @ Tue, 30 Jun 2020 00:14:21: start X-correlation... INFO @ Tue, 30 Jun 2020 00:14:21: end of X-cor INFO @ Tue, 30 Jun 2020 00:14:21: #2 finished! INFO @ Tue, 30 Jun 2020 00:14:21: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 00:14:21: #2 alternative fragment length(s) may be 4,45 bps INFO @ Tue, 30 Jun 2020 00:14:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.05_model.r WARNING @ Tue, 30 Jun 2020 00:14:21: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:14:21: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Tue, 30 Jun 2020 00:14:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:14:21: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:14:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:14:21: 12000000 INFO @ Tue, 30 Jun 2020 00:14:26: 8000000 INFO @ Tue, 30 Jun 2020 00:14:28: 13000000 INFO @ Tue, 30 Jun 2020 00:14:32: 9000000 INFO @ Tue, 30 Jun 2020 00:14:34: 14000000 INFO @ Tue, 30 Jun 2020 00:14:39: 10000000 INFO @ Tue, 30 Jun 2020 00:14:41: 15000000 INFO @ Tue, 30 Jun 2020 00:14:46: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:14:47: 16000000 INFO @ Tue, 30 Jun 2020 00:14:51: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:14:51: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:14:51: #1 total tags in treatment: 16558062 INFO @ Tue, 30 Jun 2020 00:14:51: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:14:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:14:51: #1 tags after filtering in treatment: 16558062 INFO @ Tue, 30 Jun 2020 00:14:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:14:51: #1 finished! INFO @ Tue, 30 Jun 2020 00:14:51: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:14:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:14:52: 12000000 INFO @ Tue, 30 Jun 2020 00:14:52: #2 number of paired peaks: 140 WARNING @ Tue, 30 Jun 2020 00:14:52: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 30 Jun 2020 00:14:52: start model_add_line... INFO @ Tue, 30 Jun 2020 00:14:52: start X-correlation... INFO @ Tue, 30 Jun 2020 00:14:52: end of X-cor INFO @ Tue, 30 Jun 2020 00:14:52: #2 finished! INFO @ Tue, 30 Jun 2020 00:14:52: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 00:14:52: #2 alternative fragment length(s) may be 4,45 bps INFO @ Tue, 30 Jun 2020 00:14:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.10_model.r WARNING @ Tue, 30 Jun 2020 00:14:52: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:14:52: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Tue, 30 Jun 2020 00:14:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:14:52: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:14:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:14:53: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:14:58: 13000000 INFO @ Tue, 30 Jun 2020 00:15:05: 14000000 INFO @ Tue, 30 Jun 2020 00:15:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:15:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:15:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.05_summits.bed INFO @ Tue, 30 Jun 2020 00:15:10: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8804 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:15:11: 15000000 INFO @ Tue, 30 Jun 2020 00:15:17: 16000000 INFO @ Tue, 30 Jun 2020 00:15:20: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:15:20: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:15:20: #1 total tags in treatment: 16558062 INFO @ Tue, 30 Jun 2020 00:15:20: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:15:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:15:21: #1 tags after filtering in treatment: 16558062 INFO @ Tue, 30 Jun 2020 00:15:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:15:21: #1 finished! INFO @ Tue, 30 Jun 2020 00:15:21: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:15:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:15:22: #2 number of paired peaks: 140 WARNING @ Tue, 30 Jun 2020 00:15:22: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 30 Jun 2020 00:15:22: start model_add_line... INFO @ Tue, 30 Jun 2020 00:15:22: start X-correlation... INFO @ Tue, 30 Jun 2020 00:15:22: end of X-cor INFO @ Tue, 30 Jun 2020 00:15:22: #2 finished! INFO @ Tue, 30 Jun 2020 00:15:22: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 00:15:22: #2 alternative fragment length(s) may be 4,45 bps INFO @ Tue, 30 Jun 2020 00:15:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.20_model.r WARNING @ Tue, 30 Jun 2020 00:15:22: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:15:22: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Tue, 30 Jun 2020 00:15:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:15:22: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:15:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:15:24: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:15:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:15:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:15:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.10_summits.bed INFO @ Tue, 30 Jun 2020 00:15:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2144 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:15:55: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:16:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:16:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:16:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467060/SRX467060.20_summits.bed INFO @ Tue, 30 Jun 2020 00:16:12: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (770 records, 4 fields): 2 millis CompletedMACS2peakCalling