Job ID = 6527848 SRX = SRX287865 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:47:30 prefetch.2.10.7: 1) Downloading 'SRR870054'... 2020-06-29T13:47:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:51:19 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:51:19 prefetch.2.10.7: 1) 'SRR870054' was downloaded successfully Read 19240980 spots for SRR870054/SRR870054.sra Written 19240980 spots for SRR870054/SRR870054.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: 00:07:00 19240980 reads; of these: 19240980 (100.00%) were unpaired; of these: 903684 (4.70%) aligned 0 times 12171541 (63.26%) aligned exactly 1 time 6165755 (32.04%) aligned >1 times 95.30% overall alignment rate Time searching: 00:07:00 Overall time: 00:07:00 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 8 files... [bam_rmdupse_core] 2074917 / 18337296 = 0.1132 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 @ Mon, 29 Jun 2020 23:08:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.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 @ Mon, 29 Jun 2020 23:08:03: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:08:03: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:08:09: 1000000 INFO @ Mon, 29 Jun 2020 23:08:14: 2000000 INFO @ Mon, 29 Jun 2020 23:08:20: 3000000 INFO @ Mon, 29 Jun 2020 23:08:26: 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 @ Mon, 29 Jun 2020 23:08:31: 5000000 INFO @ Mon, 29 Jun 2020 23:08:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.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 @ Mon, 29 Jun 2020 23:08:33: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:08:33: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:08:37: 6000000 INFO @ Mon, 29 Jun 2020 23:08:39: 1000000 INFO @ Mon, 29 Jun 2020 23:08:43: 7000000 INFO @ Mon, 29 Jun 2020 23:08:45: 2000000 INFO @ Mon, 29 Jun 2020 23:08:49: 8000000 INFO @ Mon, 29 Jun 2020 23:08:52: 3000000 INFO @ Mon, 29 Jun 2020 23:08:55: 9000000 INFO @ Mon, 29 Jun 2020 23:08:58: 4000000 INFO @ Mon, 29 Jun 2020 23:09:01: 10000000 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 @ Mon, 29 Jun 2020 23:09:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.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 @ Mon, 29 Jun 2020 23:09:03: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:09:03: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:09:05: 5000000 INFO @ Mon, 29 Jun 2020 23:09:07: 11000000 INFO @ Mon, 29 Jun 2020 23:09:08: 1000000 INFO @ Mon, 29 Jun 2020 23:09:11: 6000000 INFO @ Mon, 29 Jun 2020 23:09:13: 12000000 INFO @ Mon, 29 Jun 2020 23:09:14: 2000000 INFO @ Mon, 29 Jun 2020 23:09:17: 7000000 INFO @ Mon, 29 Jun 2020 23:09:19: 13000000 INFO @ Mon, 29 Jun 2020 23:09:19: 3000000 INFO @ Mon, 29 Jun 2020 23:09:23: 8000000 INFO @ Mon, 29 Jun 2020 23:09:24: 4000000 INFO @ Mon, 29 Jun 2020 23:09:25: 14000000 INFO @ Mon, 29 Jun 2020 23:09:29: 9000000 INFO @ Mon, 29 Jun 2020 23:09:30: 5000000 INFO @ Mon, 29 Jun 2020 23:09:31: 15000000 INFO @ Mon, 29 Jun 2020 23:09:35: 10000000 INFO @ Mon, 29 Jun 2020 23:09:35: 6000000 INFO @ Mon, 29 Jun 2020 23:09:37: 16000000 INFO @ Mon, 29 Jun 2020 23:09:38: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:09:38: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:09:38: #1 total tags in treatment: 16262379 INFO @ Mon, 29 Jun 2020 23:09:38: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:09:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:09:39: #1 tags after filtering in treatment: 16262379 INFO @ Mon, 29 Jun 2020 23:09:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:09:39: #1 finished! INFO @ Mon, 29 Jun 2020 23:09:39: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:09:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:09:40: #2 number of paired peaks: 243 WARNING @ Mon, 29 Jun 2020 23:09:40: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Mon, 29 Jun 2020 23:09:40: start model_add_line... INFO @ Mon, 29 Jun 2020 23:09:40: start X-correlation... INFO @ Mon, 29 Jun 2020 23:09:40: end of X-cor INFO @ Mon, 29 Jun 2020 23:09:40: #2 finished! INFO @ Mon, 29 Jun 2020 23:09:40: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 23:09:40: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 29 Jun 2020 23:09:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.05_model.r WARNING @ Mon, 29 Jun 2020 23:09:40: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:09:40: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 29 Jun 2020 23:09:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:09:40: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:09:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:09:41: 7000000 INFO @ Mon, 29 Jun 2020 23:09:41: 11000000 INFO @ Mon, 29 Jun 2020 23:09:46: 8000000 INFO @ Mon, 29 Jun 2020 23:09:47: 12000000 INFO @ Mon, 29 Jun 2020 23:09:51: 9000000 INFO @ Mon, 29 Jun 2020 23:09:53: 13000000 INFO @ Mon, 29 Jun 2020 23:09:57: 10000000 INFO @ Mon, 29 Jun 2020 23:09:59: 14000000 INFO @ Mon, 29 Jun 2020 23:10:02: 11000000 INFO @ Mon, 29 Jun 2020 23:10:05: 15000000 INFO @ Mon, 29 Jun 2020 23:10:07: 12000000 INFO @ Mon, 29 Jun 2020 23:10:10: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:10:11: 16000000 INFO @ Mon, 29 Jun 2020 23:10:13: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:10:13: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:10:13: #1 total tags in treatment: 16262379 INFO @ Mon, 29 Jun 2020 23:10:13: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:10:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:10:13: 13000000 INFO @ Mon, 29 Jun 2020 23:10:13: #1 tags after filtering in treatment: 16262379 INFO @ Mon, 29 Jun 2020 23:10:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:10:13: #1 finished! INFO @ Mon, 29 Jun 2020 23:10:13: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:10:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:10:14: #2 number of paired peaks: 243 WARNING @ Mon, 29 Jun 2020 23:10:14: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Mon, 29 Jun 2020 23:10:14: start model_add_line... INFO @ Mon, 29 Jun 2020 23:10:14: start X-correlation... INFO @ Mon, 29 Jun 2020 23:10:14: end of X-cor INFO @ Mon, 29 Jun 2020 23:10:14: #2 finished! INFO @ Mon, 29 Jun 2020 23:10:14: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 23:10:14: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 29 Jun 2020 23:10:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.10_model.r WARNING @ Mon, 29 Jun 2020 23:10:14: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:10:14: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 29 Jun 2020 23:10:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:10:14: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:10:14: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:10:18: 14000000 INFO @ Mon, 29 Jun 2020 23:10:23: 15000000 INFO @ Mon, 29 Jun 2020 23:10:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:10:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:10:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.05_summits.bed INFO @ Mon, 29 Jun 2020 23:10:25: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2130 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:10:29: 16000000 INFO @ Mon, 29 Jun 2020 23:10:30: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:10:30: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:10:30: #1 total tags in treatment: 16262379 INFO @ Mon, 29 Jun 2020 23:10:30: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:10:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:10:30: #1 tags after filtering in treatment: 16262379 INFO @ Mon, 29 Jun 2020 23:10:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:10:30: #1 finished! INFO @ Mon, 29 Jun 2020 23:10:30: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:10:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:10:31: #2 number of paired peaks: 243 WARNING @ Mon, 29 Jun 2020 23:10:31: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Mon, 29 Jun 2020 23:10:31: start model_add_line... INFO @ Mon, 29 Jun 2020 23:10:31: start X-correlation... INFO @ Mon, 29 Jun 2020 23:10:31: end of X-cor INFO @ Mon, 29 Jun 2020 23:10:31: #2 finished! INFO @ Mon, 29 Jun 2020 23:10:31: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 23:10:31: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 29 Jun 2020 23:10:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.20_model.r WARNING @ Mon, 29 Jun 2020 23:10:31: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:10:31: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 29 Jun 2020 23:10:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:10:31: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:10:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:10:45: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:11:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:11:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:11:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.10_summits.bed INFO @ Mon, 29 Jun 2020 23:11:00: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1769 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:11:02: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:11:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:11:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:11:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287865/SRX287865.20_summits.bed INFO @ Mon, 29 Jun 2020 23:11:18: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1352 records, 4 fields): 2 millis CompletedMACS2peakCalling