Job ID = 6498450 SRX = SRX511348 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T23:57:14 prefetch.2.10.7: 1) Downloading 'SRR1217610'... 2020-06-25T23:57:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:58:31 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:58:32 prefetch.2.10.7: 'SRR1217610' is valid 2020-06-25T23:58:32 prefetch.2.10.7: 1) 'SRR1217610' was downloaded successfully Read 5966527 spots for SRR1217610/SRR1217610.sra Written 5966527 spots for SRR1217610/SRR1217610.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: 00:14:57 5966527 reads; of these: 5966527 (100.00%) were paired; of these: 206568 (3.46%) aligned concordantly 0 times 4217900 (70.69%) aligned concordantly exactly 1 time 1542059 (25.85%) aligned concordantly >1 times ---- 206568 pairs aligned concordantly 0 times; of these: 5721 (2.77%) aligned discordantly 1 time ---- 200847 pairs aligned 0 times concordantly or discordantly; of these: 401694 mates make up the pairs; of these: 251321 (62.57%) aligned 0 times 99863 (24.86%) aligned exactly 1 time 50510 (12.57%) aligned >1 times 97.89% overall alignment rate Time searching: 00:14:57 Overall time: 00:14:57 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 190907 / 5758314 = 0.0332 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 @ Fri, 26 Jun 2020 09:18:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.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 @ Fri, 26 Jun 2020 09:18:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:18:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:18:30: 1000000 INFO @ Fri, 26 Jun 2020 09:18:35: 2000000 INFO @ Fri, 26 Jun 2020 09:18:41: 3000000 INFO @ Fri, 26 Jun 2020 09:18:47: 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 @ Fri, 26 Jun 2020 09:18:52: 5000000 INFO @ Fri, 26 Jun 2020 09:18:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.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 @ Fri, 26 Jun 2020 09:18:54: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:18:54: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:18:58: 6000000 INFO @ Fri, 26 Jun 2020 09:18:59: 1000000 INFO @ Fri, 26 Jun 2020 09:19:04: 7000000 INFO @ Fri, 26 Jun 2020 09:19:06: 2000000 INFO @ Fri, 26 Jun 2020 09:19:10: 8000000 INFO @ Fri, 26 Jun 2020 09:19:12: 3000000 INFO @ Fri, 26 Jun 2020 09:19:16: 9000000 INFO @ Fri, 26 Jun 2020 09:19:18: 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 @ Fri, 26 Jun 2020 09:19:22: 10000000 INFO @ Fri, 26 Jun 2020 09:19:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.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 @ Fri, 26 Jun 2020 09:19:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:19:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:19:25: 5000000 INFO @ Fri, 26 Jun 2020 09:19:29: 11000000 INFO @ Fri, 26 Jun 2020 09:19:30: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:19:30: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:19:30: #1 total tags in treatment: 5569126 INFO @ Fri, 26 Jun 2020 09:19:30: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:19:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:19:31: #1 tags after filtering in treatment: 5213826 INFO @ Fri, 26 Jun 2020 09:19:31: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 26 Jun 2020 09:19:31: #1 finished! INFO @ Fri, 26 Jun 2020 09:19:31: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:19:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:19:31: #2 number of paired peaks: 512 WARNING @ Fri, 26 Jun 2020 09:19:31: Fewer paired peaks (512) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 512 pairs to build model! INFO @ Fri, 26 Jun 2020 09:19:31: start model_add_line... INFO @ Fri, 26 Jun 2020 09:19:31: start X-correlation... INFO @ Fri, 26 Jun 2020 09:19:31: end of X-cor INFO @ Fri, 26 Jun 2020 09:19:31: #2 finished! INFO @ Fri, 26 Jun 2020 09:19:31: #2 predicted fragment length is 110 bps INFO @ Fri, 26 Jun 2020 09:19:31: #2 alternative fragment length(s) may be 110 bps INFO @ Fri, 26 Jun 2020 09:19:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.05_model.r INFO @ Fri, 26 Jun 2020 09:19:31: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:19:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:19:31: 1000000 INFO @ Fri, 26 Jun 2020 09:19:32: 6000000 INFO @ Fri, 26 Jun 2020 09:19:38: 2000000 INFO @ Fri, 26 Jun 2020 09:19:39: 7000000 INFO @ Fri, 26 Jun 2020 09:19:41: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:19:45: 3000000 INFO @ Fri, 26 Jun 2020 09:19:46: 8000000 INFO @ Fri, 26 Jun 2020 09:19:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:19:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:19:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.05_summits.bed INFO @ Fri, 26 Jun 2020 09:19:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2125 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:19:52: 9000000 INFO @ Fri, 26 Jun 2020 09:19:52: 4000000 INFO @ Fri, 26 Jun 2020 09:19:58: 10000000 INFO @ Fri, 26 Jun 2020 09:20:00: 5000000 INFO @ Fri, 26 Jun 2020 09:20:05: 11000000 INFO @ Fri, 26 Jun 2020 09:20:07: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:20:07: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:20:07: #1 total tags in treatment: 5569126 INFO @ Fri, 26 Jun 2020 09:20:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:20:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:20:07: #1 tags after filtering in treatment: 5213826 INFO @ Fri, 26 Jun 2020 09:20:07: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 26 Jun 2020 09:20:07: #1 finished! INFO @ Fri, 26 Jun 2020 09:20:07: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:20:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:20:08: #2 number of paired peaks: 512 WARNING @ Fri, 26 Jun 2020 09:20:08: Fewer paired peaks (512) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 512 pairs to build model! INFO @ Fri, 26 Jun 2020 09:20:08: start model_add_line... INFO @ Fri, 26 Jun 2020 09:20:08: start X-correlation... INFO @ Fri, 26 Jun 2020 09:20:08: end of X-cor INFO @ Fri, 26 Jun 2020 09:20:08: #2 finished! INFO @ Fri, 26 Jun 2020 09:20:08: #2 predicted fragment length is 110 bps INFO @ Fri, 26 Jun 2020 09:20:08: #2 alternative fragment length(s) may be 110 bps INFO @ Fri, 26 Jun 2020 09:20:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.10_model.r INFO @ Fri, 26 Jun 2020 09:20:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:20:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:20:08: 6000000 INFO @ Fri, 26 Jun 2020 09:20:15: 7000000 INFO @ Fri, 26 Jun 2020 09:20:18: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:20:21: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:20:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:20:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:20:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.10_summits.bed INFO @ Fri, 26 Jun 2020 09:20:24: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1001 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:20:28: 9000000 INFO @ Fri, 26 Jun 2020 09:20:35: 10000000 INFO @ Fri, 26 Jun 2020 09:20:41: 11000000 INFO @ Fri, 26 Jun 2020 09:20:43: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:20:43: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:20:43: #1 total tags in treatment: 5569126 INFO @ Fri, 26 Jun 2020 09:20:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:20:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:20:43: #1 tags after filtering in treatment: 5213826 INFO @ Fri, 26 Jun 2020 09:20:43: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 26 Jun 2020 09:20:43: #1 finished! INFO @ Fri, 26 Jun 2020 09:20:43: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:20:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:20:44: #2 number of paired peaks: 512 WARNING @ Fri, 26 Jun 2020 09:20:44: Fewer paired peaks (512) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 512 pairs to build model! INFO @ Fri, 26 Jun 2020 09:20:44: start model_add_line... INFO @ Fri, 26 Jun 2020 09:20:44: start X-correlation... INFO @ Fri, 26 Jun 2020 09:20:44: end of X-cor INFO @ Fri, 26 Jun 2020 09:20:44: #2 finished! INFO @ Fri, 26 Jun 2020 09:20:44: #2 predicted fragment length is 110 bps INFO @ Fri, 26 Jun 2020 09:20:44: #2 alternative fragment length(s) may be 110 bps INFO @ Fri, 26 Jun 2020 09:20:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.20_model.r INFO @ Fri, 26 Jun 2020 09:20:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:20:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:20:54: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:21:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:21:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:21:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511348/SRX511348.20_summits.bed INFO @ Fri, 26 Jun 2020 09:21:00: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (531 records, 4 fields): 7 millis CompletedMACS2peakCalling