Job ID = 6498608 SRX = SRX645117 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T00:08:35 prefetch.2.10.7: 1) Downloading 'SRR1505717'... 2020-06-26T00:08:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:13:15 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:13:15 prefetch.2.10.7: 1) 'SRR1505717' was downloaded successfully Read 22213587 spots for SRR1505717/SRR1505717.sra Written 22213587 spots for SRR1505717/SRR1505717.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: 00:08:24 22213587 reads; of these: 22213587 (100.00%) were unpaired; of these: 14938464 (67.25%) aligned 0 times 5977456 (26.91%) aligned exactly 1 time 1297667 (5.84%) aligned >1 times 32.75% overall alignment rate Time searching: 00:08:24 Overall time: 00:08:24 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_rmdupse_core] 3839101 / 7275123 = 0.5277 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 09:26:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.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 09:26:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:26:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:26:25: 1000000 INFO @ Fri, 26 Jun 2020 09:26:33: 2000000 INFO @ Fri, 26 Jun 2020 09:26:41: 3000000 INFO @ Fri, 26 Jun 2020 09:26:44: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:26:44: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:26:44: #1 total tags in treatment: 3436022 INFO @ Fri, 26 Jun 2020 09:26:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:26:44: #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 09:26:44: #1 tags after filtering in treatment: 3436022 INFO @ Fri, 26 Jun 2020 09:26:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:26:44: #1 finished! INFO @ Fri, 26 Jun 2020 09:26:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:26:44: #2 looking for paired plus/minus strand peaks... 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 09:26:45: #2 number of paired peaks: 3408 INFO @ Fri, 26 Jun 2020 09:26:45: start model_add_line... INFO @ Fri, 26 Jun 2020 09:26:45: start X-correlation... INFO @ Fri, 26 Jun 2020 09:26:45: end of X-cor INFO @ Fri, 26 Jun 2020 09:26:45: #2 finished! INFO @ Fri, 26 Jun 2020 09:26:45: #2 predicted fragment length is 125 bps INFO @ Fri, 26 Jun 2020 09:26:45: #2 alternative fragment length(s) may be 125 bps INFO @ Fri, 26 Jun 2020 09:26:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.05_model.r WARNING @ Fri, 26 Jun 2020 09:26:45: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:26:45: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Fri, 26 Jun 2020 09:26:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:26:45: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:26:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:26:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.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 09:26:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:26:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:26:55: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:26:55: 1000000 INFO @ Fri, 26 Jun 2020 09:27:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:27:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:27:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.05_summits.bed INFO @ Fri, 26 Jun 2020 09:27:00: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5391 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:27:04: 2000000 INFO @ Fri, 26 Jun 2020 09:27:13: 3000000 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 09:27:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.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 09:27:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:27:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:27:17: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:27:17: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:27:17: #1 total tags in treatment: 3436022 INFO @ Fri, 26 Jun 2020 09:27:17: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:27:17: #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 09:27:17: #1 tags after filtering in treatment: 3436022 INFO @ Fri, 26 Jun 2020 09:27:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:27:17: #1 finished! INFO @ Fri, 26 Jun 2020 09:27:17: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:27:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:27:17: #2 number of paired peaks: 3408 INFO @ Fri, 26 Jun 2020 09:27:17: start model_add_line... INFO @ Fri, 26 Jun 2020 09:27:17: start X-correlation... INFO @ Fri, 26 Jun 2020 09:27:18: end of X-cor INFO @ Fri, 26 Jun 2020 09:27:18: #2 finished! INFO @ Fri, 26 Jun 2020 09:27:18: #2 predicted fragment length is 125 bps INFO @ Fri, 26 Jun 2020 09:27:18: #2 alternative fragment length(s) may be 125 bps INFO @ Fri, 26 Jun 2020 09:27:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.10_model.r WARNING @ Fri, 26 Jun 2020 09:27:18: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:27:18: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Fri, 26 Jun 2020 09:27:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:27:18: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:27:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:27:25: 1000000 INFO @ Fri, 26 Jun 2020 09:27:27: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:27:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:27:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:27:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.10_summits.bed INFO @ Fri, 26 Jun 2020 09:27:32: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2609 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:27:32: 2000000 INFO @ Fri, 26 Jun 2020 09:27:40: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:27:43: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:27:43: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:27:43: #1 total tags in treatment: 3436022 INFO @ Fri, 26 Jun 2020 09:27:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:27:43: #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 09:27:43: #1 tags after filtering in treatment: 3436022 INFO @ Fri, 26 Jun 2020 09:27:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:27:43: #1 finished! INFO @ Fri, 26 Jun 2020 09:27:43: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:27:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:27:44: #2 number of paired peaks: 3408 INFO @ Fri, 26 Jun 2020 09:27:44: start model_add_line... INFO @ Fri, 26 Jun 2020 09:27:44: start X-correlation... INFO @ Fri, 26 Jun 2020 09:27:44: end of X-cor INFO @ Fri, 26 Jun 2020 09:27:44: #2 finished! INFO @ Fri, 26 Jun 2020 09:27:44: #2 predicted fragment length is 125 bps INFO @ Fri, 26 Jun 2020 09:27:44: #2 alternative fragment length(s) may be 125 bps INFO @ Fri, 26 Jun 2020 09:27:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.20_model.r WARNING @ Fri, 26 Jun 2020 09:27:44: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:27:44: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Fri, 26 Jun 2020 09:27:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:27:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:27:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:27:54: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:27:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:27:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:27:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645117/SRX645117.20_summits.bed INFO @ Fri, 26 Jun 2020 09:27:58: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (783 records, 4 fields): 3 millis CompletedMACS2peakCalling