Job ID = 6458337 SRX = SRX5011083 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:48:10 prefetch.2.10.7: 1) Downloading 'SRR8191532'... 2020-06-21T12:48:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:51:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:51:21 prefetch.2.10.7: 1) 'SRR8191532' was downloaded successfully Read 21996208 spots for SRR8191532/SRR8191532.sra Written 21996208 spots for SRR8191532/SRR8191532.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: 00:05:27 21996208 reads; of these: 21996208 (100.00%) were unpaired; of these: 3363561 (15.29%) aligned 0 times 14174038 (64.44%) aligned exactly 1 time 4458609 (20.27%) aligned >1 times 84.71% overall alignment rate Time searching: 00:05:27 Overall time: 00:05:27 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 8 files... [bam_rmdupse_core] 5126241 / 18632647 = 0.2751 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 22:03:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.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 22:03:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:03:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:03:19: 1000000 INFO @ Sun, 21 Jun 2020 22:03:24: 2000000 INFO @ Sun, 21 Jun 2020 22:03:30: 3000000 INFO @ Sun, 21 Jun 2020 22:03:35: 4000000 INFO @ Sun, 21 Jun 2020 22:03:40: 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 22:03:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.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 22:03:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:03:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:03:45: 6000000 INFO @ Sun, 21 Jun 2020 22:03:50: 1000000 INFO @ Sun, 21 Jun 2020 22:03:51: 7000000 INFO @ Sun, 21 Jun 2020 22:03:56: 2000000 INFO @ Sun, 21 Jun 2020 22:03:56: 8000000 INFO @ Sun, 21 Jun 2020 22:04:01: 9000000 INFO @ Sun, 21 Jun 2020 22:04:02: 3000000 INFO @ Sun, 21 Jun 2020 22:04:07: 10000000 INFO @ Sun, 21 Jun 2020 22:04:07: 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 22:04:13: 5000000 INFO @ Sun, 21 Jun 2020 22:04:13: 11000000 INFO @ Sun, 21 Jun 2020 22:04:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.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 22:04:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:04:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:04:19: 6000000 INFO @ Sun, 21 Jun 2020 22:04:19: 12000000 INFO @ Sun, 21 Jun 2020 22:04:20: 1000000 INFO @ Sun, 21 Jun 2020 22:04:25: 7000000 INFO @ Sun, 21 Jun 2020 22:04:25: 13000000 INFO @ Sun, 21 Jun 2020 22:04:26: 2000000 INFO @ Sun, 21 Jun 2020 22:04:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:04:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:04:29: #1 total tags in treatment: 13506406 INFO @ Sun, 21 Jun 2020 22:04:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:04:29: #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 22:04:29: #1 tags after filtering in treatment: 13506292 INFO @ Sun, 21 Jun 2020 22:04:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:04:29: #1 finished! INFO @ Sun, 21 Jun 2020 22:04:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:04:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:04:30: 8000000 INFO @ Sun, 21 Jun 2020 22:04:30: #2 number of paired peaks: 977 WARNING @ Sun, 21 Jun 2020 22:04:30: Fewer paired peaks (977) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 977 pairs to build model! INFO @ Sun, 21 Jun 2020 22:04:30: start model_add_line... INFO @ Sun, 21 Jun 2020 22:04:30: start X-correlation... INFO @ Sun, 21 Jun 2020 22:04:30: end of X-cor INFO @ Sun, 21 Jun 2020 22:04:30: #2 finished! INFO @ Sun, 21 Jun 2020 22:04:30: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 22:04:30: #2 alternative fragment length(s) may be 4,100,109 bps INFO @ Sun, 21 Jun 2020 22:04:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.05_model.r WARNING @ Sun, 21 Jun 2020 22:04:30: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:04:30: #2 You may need to consider one of the other alternative d(s): 4,100,109 WARNING @ Sun, 21 Jun 2020 22:04:30: #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 22:04:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:04:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:04:32: 3000000 INFO @ Sun, 21 Jun 2020 22:04:35: 9000000 INFO @ Sun, 21 Jun 2020 22:04:38: 4000000 INFO @ Sun, 21 Jun 2020 22:04:41: 10000000 INFO @ Sun, 21 Jun 2020 22:04:44: 5000000 INFO @ Sun, 21 Jun 2020 22:04:47: 11000000 INFO @ Sun, 21 Jun 2020 22:04:49: 6000000 INFO @ Sun, 21 Jun 2020 22:04:52: 12000000 INFO @ Sun, 21 Jun 2020 22:04:55: 7000000 INFO @ Sun, 21 Jun 2020 22:04:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:04:57: 13000000 INFO @ Sun, 21 Jun 2020 22:05:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:05:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:05:00: #1 total tags in treatment: 13506406 INFO @ Sun, 21 Jun 2020 22:05:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:05:00: #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 22:05:01: 8000000 INFO @ Sun, 21 Jun 2020 22:05:01: #1 tags after filtering in treatment: 13506292 INFO @ Sun, 21 Jun 2020 22:05:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:05:01: #1 finished! INFO @ Sun, 21 Jun 2020 22:05:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:05:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:05:02: #2 number of paired peaks: 977 WARNING @ Sun, 21 Jun 2020 22:05:02: Fewer paired peaks (977) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 977 pairs to build model! INFO @ Sun, 21 Jun 2020 22:05:02: start model_add_line... INFO @ Sun, 21 Jun 2020 22:05:02: start X-correlation... INFO @ Sun, 21 Jun 2020 22:05:02: end of X-cor INFO @ Sun, 21 Jun 2020 22:05:02: #2 finished! INFO @ Sun, 21 Jun 2020 22:05:02: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 22:05:02: #2 alternative fragment length(s) may be 4,100,109 bps INFO @ Sun, 21 Jun 2020 22:05:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.10_model.r WARNING @ Sun, 21 Jun 2020 22:05:02: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:05:02: #2 You may need to consider one of the other alternative d(s): 4,100,109 WARNING @ Sun, 21 Jun 2020 22:05:02: #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 22:05:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:05:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:05:07: 9000000 INFO @ Sun, 21 Jun 2020 22:05:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:05:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:05:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.05_summits.bed INFO @ Sun, 21 Jun 2020 22:05:10: Done! pass1 - making usageList (586 chroms): 2 millis pass2 - checking and writing primary data (3088 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:05:12: 10000000 INFO @ Sun, 21 Jun 2020 22:05:19: 11000000 INFO @ Sun, 21 Jun 2020 22:05:24: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:05:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:05:30: 13000000 INFO @ Sun, 21 Jun 2020 22:05:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:05:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:05:33: #1 total tags in treatment: 13506406 INFO @ Sun, 21 Jun 2020 22:05:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:05:33: #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 22:05:34: #1 tags after filtering in treatment: 13506292 INFO @ Sun, 21 Jun 2020 22:05:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:05:34: #1 finished! INFO @ Sun, 21 Jun 2020 22:05:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:05:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:05:35: #2 number of paired peaks: 977 WARNING @ Sun, 21 Jun 2020 22:05:35: Fewer paired peaks (977) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 977 pairs to build model! INFO @ Sun, 21 Jun 2020 22:05:35: start model_add_line... INFO @ Sun, 21 Jun 2020 22:05:35: start X-correlation... INFO @ Sun, 21 Jun 2020 22:05:35: end of X-cor INFO @ Sun, 21 Jun 2020 22:05:35: #2 finished! INFO @ Sun, 21 Jun 2020 22:05:35: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 22:05:35: #2 alternative fragment length(s) may be 4,100,109 bps INFO @ Sun, 21 Jun 2020 22:05:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.20_model.r WARNING @ Sun, 21 Jun 2020 22:05:35: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:05:35: #2 You may need to consider one of the other alternative d(s): 4,100,109 WARNING @ Sun, 21 Jun 2020 22:05:35: #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 22:05:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:05:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:05:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:05:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:05:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.10_summits.bed INFO @ Sun, 21 Jun 2020 22:05:41: Done! pass1 - making usageList (410 chroms): 1 millis pass2 - checking and writing primary data (1871 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:06:02: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:06:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:06:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:06:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011083/SRX5011083.20_summits.bed INFO @ Sun, 21 Jun 2020 22:06:16: Done! pass1 - making usageList (294 chroms): 1 millis pass2 - checking and writing primary data (960 records, 4 fields): 18 millis CompletedMACS2peakCalling