Job ID = 6458813 SRX = SRX5535385 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:37:41 prefetch.2.10.7: 1) Downloading 'SRR8743313'... 2020-06-21T12:37:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:39:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:39:26 prefetch.2.10.7: 1) 'SRR8743313' was downloaded successfully Read 22790183 spots for SRR8743313/SRR8743313.sra Written 22790183 spots for SRR8743313/SRR8743313.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: 00:06:15 22790183 reads; of these: 22790183 (100.00%) were unpaired; of these: 973601 (4.27%) aligned 0 times 13782541 (60.48%) aligned exactly 1 time 8034041 (35.25%) aligned >1 times 95.73% overall alignment rate Time searching: 00:06:16 Overall time: 00:06:16 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] 6722183 / 21816582 = 0.3081 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 21:50:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.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 21:50:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:50:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:51:00: 1000000 INFO @ Sun, 21 Jun 2020 21:51:05: 2000000 INFO @ Sun, 21 Jun 2020 21:51:10: 3000000 INFO @ Sun, 21 Jun 2020 21:51:14: 4000000 INFO @ Sun, 21 Jun 2020 21:51:19: 5000000 INFO @ Sun, 21 Jun 2020 21:51:24: 6000000 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 21:51:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.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 21:51:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:51:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:51:29: 7000000 INFO @ Sun, 21 Jun 2020 21:51:31: 1000000 INFO @ Sun, 21 Jun 2020 21:51:34: 8000000 INFO @ Sun, 21 Jun 2020 21:51:35: 2000000 INFO @ Sun, 21 Jun 2020 21:51:38: 9000000 INFO @ Sun, 21 Jun 2020 21:51:40: 3000000 INFO @ Sun, 21 Jun 2020 21:51:43: 10000000 INFO @ Sun, 21 Jun 2020 21:51:45: 4000000 INFO @ Sun, 21 Jun 2020 21:51:48: 11000000 INFO @ Sun, 21 Jun 2020 21:51:50: 5000000 INFO @ Sun, 21 Jun 2020 21:51:53: 12000000 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 21:51:55: 6000000 INFO @ Sun, 21 Jun 2020 21:51:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.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 21:51:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:51:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:51:59: 13000000 INFO @ Sun, 21 Jun 2020 21:52:00: 7000000 INFO @ Sun, 21 Jun 2020 21:52:01: 1000000 INFO @ Sun, 21 Jun 2020 21:52:04: 14000000 INFO @ Sun, 21 Jun 2020 21:52:05: 8000000 INFO @ Sun, 21 Jun 2020 21:52:07: 2000000 INFO @ Sun, 21 Jun 2020 21:52:09: 15000000 INFO @ Sun, 21 Jun 2020 21:52:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:52:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:52:09: #1 total tags in treatment: 15094399 INFO @ Sun, 21 Jun 2020 21:52:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:52:09: #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 21:52:10: #1 tags after filtering in treatment: 15094334 INFO @ Sun, 21 Jun 2020 21:52:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:52:10: #1 finished! INFO @ Sun, 21 Jun 2020 21:52:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:52:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:52:11: 9000000 INFO @ Sun, 21 Jun 2020 21:52:11: #2 number of paired peaks: 642 WARNING @ Sun, 21 Jun 2020 21:52:11: Fewer paired peaks (642) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 642 pairs to build model! INFO @ Sun, 21 Jun 2020 21:52:11: start model_add_line... INFO @ Sun, 21 Jun 2020 21:52:11: start X-correlation... INFO @ Sun, 21 Jun 2020 21:52:11: end of X-cor INFO @ Sun, 21 Jun 2020 21:52:11: #2 finished! INFO @ Sun, 21 Jun 2020 21:52:11: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 21:52:11: #2 alternative fragment length(s) may be 0,50,77,133,523,575 bps INFO @ Sun, 21 Jun 2020 21:52:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.05_model.r WARNING @ Sun, 21 Jun 2020 21:52:11: #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 21:52:11: #2 You may need to consider one of the other alternative d(s): 0,50,77,133,523,575 WARNING @ Sun, 21 Jun 2020 21:52:11: #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 21:52:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:52:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:52:13: 3000000 INFO @ Sun, 21 Jun 2020 21:52:16: 10000000 INFO @ Sun, 21 Jun 2020 21:52:19: 4000000 INFO @ Sun, 21 Jun 2020 21:52:21: 11000000 INFO @ Sun, 21 Jun 2020 21:52:25: 5000000 INFO @ Sun, 21 Jun 2020 21:52:26: 12000000 INFO @ Sun, 21 Jun 2020 21:52:30: 6000000 INFO @ Sun, 21 Jun 2020 21:52:31: 13000000 INFO @ Sun, 21 Jun 2020 21:52:36: 7000000 INFO @ Sun, 21 Jun 2020 21:52:36: 14000000 INFO @ Sun, 21 Jun 2020 21:52:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:52:42: 15000000 INFO @ Sun, 21 Jun 2020 21:52:42: 8000000 INFO @ Sun, 21 Jun 2020 21:52:42: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:52:42: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:52:42: #1 total tags in treatment: 15094399 INFO @ Sun, 21 Jun 2020 21:52:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:52:42: #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 21:52:43: #1 tags after filtering in treatment: 15094334 INFO @ Sun, 21 Jun 2020 21:52:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:52:43: #1 finished! INFO @ Sun, 21 Jun 2020 21:52:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:52:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:52:44: #2 number of paired peaks: 642 WARNING @ Sun, 21 Jun 2020 21:52:44: Fewer paired peaks (642) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 642 pairs to build model! INFO @ Sun, 21 Jun 2020 21:52:44: start model_add_line... INFO @ Sun, 21 Jun 2020 21:52:44: start X-correlation... INFO @ Sun, 21 Jun 2020 21:52:44: end of X-cor INFO @ Sun, 21 Jun 2020 21:52:44: #2 finished! INFO @ Sun, 21 Jun 2020 21:52:44: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 21:52:44: #2 alternative fragment length(s) may be 0,50,77,133,523,575 bps INFO @ Sun, 21 Jun 2020 21:52:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.10_model.r WARNING @ Sun, 21 Jun 2020 21:52:44: #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 21:52:44: #2 You may need to consider one of the other alternative d(s): 0,50,77,133,523,575 WARNING @ Sun, 21 Jun 2020 21:52:44: #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 21:52:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:52:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:52:48: 9000000 INFO @ Sun, 21 Jun 2020 21:52:54: 10000000 INFO @ Sun, 21 Jun 2020 21:52:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:52:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:52:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.05_summits.bed INFO @ Sun, 21 Jun 2020 21:52:56: Done! pass1 - making usageList (522 chroms): 2 millis pass2 - checking and writing primary data (2203 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:52:59: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:53:05: 12000000 INFO @ Sun, 21 Jun 2020 21:53:11: 13000000 INFO @ Sun, 21 Jun 2020 21:53:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:53:17: 14000000 INFO @ Sun, 21 Jun 2020 21:53:23: 15000000 INFO @ Sun, 21 Jun 2020 21:53:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:53:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:53:24: #1 total tags in treatment: 15094399 INFO @ Sun, 21 Jun 2020 21:53:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:53:24: #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 21:53:24: #1 tags after filtering in treatment: 15094334 INFO @ Sun, 21 Jun 2020 21:53:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:53:24: #1 finished! INFO @ Sun, 21 Jun 2020 21:53:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:53:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:53:25: #2 number of paired peaks: 642 WARNING @ Sun, 21 Jun 2020 21:53:25: Fewer paired peaks (642) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 642 pairs to build model! INFO @ Sun, 21 Jun 2020 21:53:25: start model_add_line... INFO @ Sun, 21 Jun 2020 21:53:25: start X-correlation... INFO @ Sun, 21 Jun 2020 21:53:25: end of X-cor INFO @ Sun, 21 Jun 2020 21:53:25: #2 finished! INFO @ Sun, 21 Jun 2020 21:53:25: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 21:53:25: #2 alternative fragment length(s) may be 0,50,77,133,523,575 bps INFO @ Sun, 21 Jun 2020 21:53:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.20_model.r WARNING @ Sun, 21 Jun 2020 21:53:25: #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 21:53:25: #2 You may need to consider one of the other alternative d(s): 0,50,77,133,523,575 WARNING @ Sun, 21 Jun 2020 21:53:25: #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 21:53:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:53:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:53:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:53:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:53:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.10_summits.bed INFO @ Sun, 21 Jun 2020 21:53:29: Done! pass1 - making usageList (390 chroms): 1 millis pass2 - checking and writing primary data (1051 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:53:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:54:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:54:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:54:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5535385/SRX5535385.20_summits.bed INFO @ Sun, 21 Jun 2020 21:54:11: Done! pass1 - making usageList (83 chroms): 0 millis pass2 - checking and writing primary data (147 records, 4 fields): 4 millis CompletedMACS2peakCalling