Job ID = 6459821 SRX = SRX864530 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:41:02 prefetch.2.10.7: 1) Downloading 'SRR1785670'... 2020-06-21T13:41:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:42:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:42:24 prefetch.2.10.7: 'SRR1785670' is valid 2020-06-21T13:42:24 prefetch.2.10.7: 1) 'SRR1785670' was downloaded successfully 2020-06-21T13:42:24 prefetch.2.10.7: 'SRR1785670' has 0 unresolved dependencies Read 5833594 spots for SRR1785670/SRR1785670.sra Written 5833594 spots for SRR1785670/SRR1785670.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: 00:04:40 5833594 reads; of these: 5833594 (100.00%) were unpaired; of these: 118000 (2.02%) aligned 0 times 4681756 (80.26%) aligned exactly 1 time 1033838 (17.72%) aligned >1 times 97.98% overall alignment rate Time searching: 00:04:40 Overall time: 00:04:40 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 8 files... [bam_rmdupse_core] 228160 / 5715594 = 0.0399 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 22:52:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.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 22:52:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:52:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:52:30: 1000000 INFO @ Sun, 21 Jun 2020 22:52:40: 2000000 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 22:52:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.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 22:52:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:52:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:52:50: 3000000 INFO @ Sun, 21 Jun 2020 22:52:59: 1000000 INFO @ Sun, 21 Jun 2020 22:53:00: 4000000 INFO @ Sun, 21 Jun 2020 22:53:09: 2000000 INFO @ Sun, 21 Jun 2020 22:53:12: 5000000 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 22:53:19: #1 tag size is determined as 145 bps INFO @ Sun, 21 Jun 2020 22:53:19: #1 tag size = 145 INFO @ Sun, 21 Jun 2020 22:53:19: #1 total tags in treatment: 5487434 INFO @ Sun, 21 Jun 2020 22:53:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:53:19: #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 22:53:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.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 22:53:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:53:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:53:19: #1 tags after filtering in treatment: 5487179 INFO @ Sun, 21 Jun 2020 22:53:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:53:19: #1 finished! INFO @ Sun, 21 Jun 2020 22:53:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:53:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:53:19: #2 number of paired peaks: 564 WARNING @ Sun, 21 Jun 2020 22:53:19: Fewer paired peaks (564) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 564 pairs to build model! INFO @ Sun, 21 Jun 2020 22:53:19: start model_add_line... INFO @ Sun, 21 Jun 2020 22:53:20: start X-correlation... INFO @ Sun, 21 Jun 2020 22:53:20: end of X-cor INFO @ Sun, 21 Jun 2020 22:53:20: #2 finished! INFO @ Sun, 21 Jun 2020 22:53:20: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 22:53:20: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 22:53:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.05_model.r WARNING @ Sun, 21 Jun 2020 22:53:20: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:53:20: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sun, 21 Jun 2020 22:53:20: #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 22:53:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:53:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:53:20: 3000000 INFO @ Sun, 21 Jun 2020 22:53:30: 4000000 INFO @ Sun, 21 Jun 2020 22:53:31: 1000000 INFO @ Sun, 21 Jun 2020 22:53:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:53:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:53:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:53:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.05_summits.bed INFO @ Sun, 21 Jun 2020 22:53:39: Done! pass1 - making usageList (511 chroms): 1 millis pass2 - checking and writing primary data (1180 records, 4 fields): 70 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:53:41: 5000000 INFO @ Sun, 21 Jun 2020 22:53:43: 2000000 INFO @ Sun, 21 Jun 2020 22:53:46: #1 tag size is determined as 145 bps INFO @ Sun, 21 Jun 2020 22:53:46: #1 tag size = 145 INFO @ Sun, 21 Jun 2020 22:53:46: #1 total tags in treatment: 5487434 INFO @ Sun, 21 Jun 2020 22:53:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:53:46: #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 22:53:47: #1 tags after filtering in treatment: 5487179 INFO @ Sun, 21 Jun 2020 22:53:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:53:47: #1 finished! INFO @ Sun, 21 Jun 2020 22:53:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:53:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:53:47: #2 number of paired peaks: 564 WARNING @ Sun, 21 Jun 2020 22:53:47: Fewer paired peaks (564) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 564 pairs to build model! INFO @ Sun, 21 Jun 2020 22:53:47: start model_add_line... INFO @ Sun, 21 Jun 2020 22:53:47: start X-correlation... INFO @ Sun, 21 Jun 2020 22:53:47: end of X-cor INFO @ Sun, 21 Jun 2020 22:53:47: #2 finished! INFO @ Sun, 21 Jun 2020 22:53:47: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 22:53:47: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 22:53:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.10_model.r WARNING @ Sun, 21 Jun 2020 22:53:47: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:53:47: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sun, 21 Jun 2020 22:53:47: #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 22:53:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:53:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:53:53: 3000000 INFO @ Sun, 21 Jun 2020 22:53:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:54:05: 4000000 INFO @ Sun, 21 Jun 2020 22:54:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:54:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:54:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.10_summits.bed INFO @ Sun, 21 Jun 2020 22:54:06: Done! pass1 - making usageList (422 chroms): 1 millis pass2 - checking and writing primary data (818 records, 4 fields): 24 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:54:16: 5000000 INFO @ Sun, 21 Jun 2020 22:54:22: #1 tag size is determined as 145 bps INFO @ Sun, 21 Jun 2020 22:54:22: #1 tag size = 145 INFO @ Sun, 21 Jun 2020 22:54:22: #1 total tags in treatment: 5487434 INFO @ Sun, 21 Jun 2020 22:54:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:54:22: #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 22:54:22: #1 tags after filtering in treatment: 5487179 INFO @ Sun, 21 Jun 2020 22:54:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:54:22: #1 finished! INFO @ Sun, 21 Jun 2020 22:54:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:54:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:54:23: #2 number of paired peaks: 564 WARNING @ Sun, 21 Jun 2020 22:54:23: Fewer paired peaks (564) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 564 pairs to build model! INFO @ Sun, 21 Jun 2020 22:54:23: start model_add_line... INFO @ Sun, 21 Jun 2020 22:54:23: start X-correlation... INFO @ Sun, 21 Jun 2020 22:54:23: end of X-cor INFO @ Sun, 21 Jun 2020 22:54:23: #2 finished! INFO @ Sun, 21 Jun 2020 22:54:23: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 22:54:23: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 22:54:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.20_model.r WARNING @ Sun, 21 Jun 2020 22:54:23: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:54:23: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sun, 21 Jun 2020 22:54:23: #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 22:54:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:54:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:54:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:54:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:54:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:54:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX864530/SRX864530.20_summits.bed INFO @ Sun, 21 Jun 2020 22:54:41: Done! pass1 - making usageList (320 chroms): 1 millis pass2 - checking and writing primary data (529 records, 4 fields): 18 millis CompletedMACS2peakCalling