Job ID = 6459868 SRX = SRX914963 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:48:19 prefetch.2.10.7: 1) Downloading 'SRR1873273'... 2020-06-21T13:48:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:49:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:49:32 prefetch.2.10.7: 'SRR1873273' is valid 2020-06-21T13:49:32 prefetch.2.10.7: 1) 'SRR1873273' was downloaded successfully Read 12300633 spots for SRR1873273/SRR1873273.sra Written 12300633 spots for SRR1873273/SRR1873273.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: 00:03:02 12300633 reads; of these: 12300633 (100.00%) were unpaired; of these: 636457 (5.17%) aligned 0 times 10313806 (83.85%) aligned exactly 1 time 1350370 (10.98%) aligned >1 times 94.83% overall alignment rate Time searching: 00:03:02 Overall time: 00:03:02 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] 2899878 / 11664176 = 0.2486 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 22:56:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.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 22:56:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:56:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:56:37: 1000000 INFO @ Sun, 21 Jun 2020 22:56:42: 2000000 INFO @ Sun, 21 Jun 2020 22:56:48: 3000000 INFO @ Sun, 21 Jun 2020 22:56:53: 4000000 INFO @ Sun, 21 Jun 2020 22:56:59: 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 22:57:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.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 22:57:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:57:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:57:04: 6000000 INFO @ Sun, 21 Jun 2020 22:57:07: 1000000 INFO @ Sun, 21 Jun 2020 22:57:10: 7000000 INFO @ Sun, 21 Jun 2020 22:57:14: 2000000 INFO @ Sun, 21 Jun 2020 22:57:17: 8000000 INFO @ Sun, 21 Jun 2020 22:57:20: 3000000 INFO @ Sun, 21 Jun 2020 22:57:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:57:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:57:21: #1 total tags in treatment: 8764298 INFO @ Sun, 21 Jun 2020 22:57:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:57:21: #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 22:57:22: #1 tags after filtering in treatment: 8764036 INFO @ Sun, 21 Jun 2020 22:57:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:57:22: #1 finished! INFO @ Sun, 21 Jun 2020 22:57:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:57:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:57:22: #2 number of paired peaks: 308 WARNING @ Sun, 21 Jun 2020 22:57:22: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Sun, 21 Jun 2020 22:57:22: start model_add_line... INFO @ Sun, 21 Jun 2020 22:57:22: start X-correlation... INFO @ Sun, 21 Jun 2020 22:57:22: end of X-cor INFO @ Sun, 21 Jun 2020 22:57:22: #2 finished! INFO @ Sun, 21 Jun 2020 22:57:22: #2 predicted fragment length is 210 bps INFO @ Sun, 21 Jun 2020 22:57:22: #2 alternative fragment length(s) may be 4,189,210 bps INFO @ Sun, 21 Jun 2020 22:57:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.05_model.r INFO @ Sun, 21 Jun 2020 22:57:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:57:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:57:26: 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 22:57:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.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 22:57:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:57:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:57:31: 5000000 INFO @ Sun, 21 Jun 2020 22:57:37: 1000000 INFO @ Sun, 21 Jun 2020 22:57:37: 6000000 INFO @ Sun, 21 Jun 2020 22:57:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:57:43: 2000000 INFO @ Sun, 21 Jun 2020 22:57:43: 7000000 INFO @ Sun, 21 Jun 2020 22:57:49: 3000000 INFO @ Sun, 21 Jun 2020 22:57:50: 8000000 INFO @ Sun, 21 Jun 2020 22:57:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:57:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:57:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.05_summits.bed INFO @ Sun, 21 Jun 2020 22:57:51: Done! pass1 - making usageList (122 chroms): 1 millis pass2 - checking and writing primary data (1223 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:57:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:57:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:57:54: #1 total tags in treatment: 8764298 INFO @ Sun, 21 Jun 2020 22:57:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:57:54: #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 22:57:55: #1 tags after filtering in treatment: 8764036 INFO @ Sun, 21 Jun 2020 22:57:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:57:55: #1 finished! INFO @ Sun, 21 Jun 2020 22:57:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:57:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:57:55: 4000000 INFO @ Sun, 21 Jun 2020 22:57:55: #2 number of paired peaks: 308 WARNING @ Sun, 21 Jun 2020 22:57:55: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Sun, 21 Jun 2020 22:57:55: start model_add_line... INFO @ Sun, 21 Jun 2020 22:57:56: start X-correlation... INFO @ Sun, 21 Jun 2020 22:57:56: end of X-cor INFO @ Sun, 21 Jun 2020 22:57:56: #2 finished! INFO @ Sun, 21 Jun 2020 22:57:56: #2 predicted fragment length is 210 bps INFO @ Sun, 21 Jun 2020 22:57:56: #2 alternative fragment length(s) may be 4,189,210 bps INFO @ Sun, 21 Jun 2020 22:57:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.10_model.r INFO @ Sun, 21 Jun 2020 22:57:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:57:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:58:01: 5000000 INFO @ Sun, 21 Jun 2020 22:58:07: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:58:12: 7000000 INFO @ Sun, 21 Jun 2020 22:58:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:58:18: 8000000 INFO @ Sun, 21 Jun 2020 22:58:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:58:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:58:22: #1 total tags in treatment: 8764298 INFO @ Sun, 21 Jun 2020 22:58:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:58:22: #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 22:58:23: #1 tags after filtering in treatment: 8764036 INFO @ Sun, 21 Jun 2020 22:58:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:58:23: #1 finished! INFO @ Sun, 21 Jun 2020 22:58:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:58:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:58:23: #2 number of paired peaks: 308 WARNING @ Sun, 21 Jun 2020 22:58:23: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Sun, 21 Jun 2020 22:58:23: start model_add_line... INFO @ Sun, 21 Jun 2020 22:58:23: start X-correlation... INFO @ Sun, 21 Jun 2020 22:58:23: end of X-cor INFO @ Sun, 21 Jun 2020 22:58:23: #2 finished! INFO @ Sun, 21 Jun 2020 22:58:23: #2 predicted fragment length is 210 bps INFO @ Sun, 21 Jun 2020 22:58:23: #2 alternative fragment length(s) may be 4,189,210 bps INFO @ Sun, 21 Jun 2020 22:58:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.20_model.r INFO @ Sun, 21 Jun 2020 22:58:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:58:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:58:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:58:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:58:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.10_summits.bed INFO @ Sun, 21 Jun 2020 22:58:26: Done! pass1 - making usageList (97 chroms): 1 millis pass2 - checking and writing primary data (263 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:58:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:58:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:58:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:58:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX914963/SRX914963.20_summits.bed INFO @ Sun, 21 Jun 2020 22:58:53: Done! pass1 - making usageList (71 chroms): 1 millis pass2 - checking and writing primary data (115 records, 4 fields): 3 millis CompletedMACS2peakCalling