Job ID = 6452497 SRX = SRX013101 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:29:04 prefetch.2.10.7: 1) Downloading 'SRR030367'... 2020-06-21T07:29:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:30:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:30:46 prefetch.2.10.7: 'SRR030367' is valid 2020-06-21T07:30:46 prefetch.2.10.7: 1) 'SRR030367' was downloaded successfully Read 8403975 spots for SRR030367/SRR030367.sra Written 8403975 spots for SRR030367/SRR030367.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: 00:02:12 8403975 reads; of these: 8403975 (100.00%) were unpaired; of these: 330284 (3.93%) aligned 0 times 4108623 (48.89%) aligned exactly 1 time 3965068 (47.18%) aligned >1 times 96.07% overall alignment rate Time searching: 00:02:12 Overall time: 00:02:12 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_rmdupse_core] 1380684 / 8073691 = 0.1710 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 16:35:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.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 16:35:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:35:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:35:31: 1000000 INFO @ Sun, 21 Jun 2020 16:35:36: 2000000 INFO @ Sun, 21 Jun 2020 16:35:41: 3000000 INFO @ Sun, 21 Jun 2020 16:35:46: 4000000 INFO @ Sun, 21 Jun 2020 16:35:51: 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 16:35:56: 6000000 INFO @ Sun, 21 Jun 2020 16:35:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.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 16:35:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:35:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:36:00: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:36:00: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:36:00: #1 total tags in treatment: 6693007 INFO @ Sun, 21 Jun 2020 16:36:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:36:00: #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 16:36:01: #1 tags after filtering in treatment: 6692990 INFO @ Sun, 21 Jun 2020 16:36:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:36:01: #1 finished! INFO @ Sun, 21 Jun 2020 16:36:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:36:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:36:01: #2 number of paired peaks: 2367 INFO @ Sun, 21 Jun 2020 16:36:01: start model_add_line... INFO @ Sun, 21 Jun 2020 16:36:01: 1000000 INFO @ Sun, 21 Jun 2020 16:36:01: start X-correlation... INFO @ Sun, 21 Jun 2020 16:36:01: end of X-cor INFO @ Sun, 21 Jun 2020 16:36:01: #2 finished! INFO @ Sun, 21 Jun 2020 16:36:01: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 16:36:01: #2 alternative fragment length(s) may be 4,46,592 bps INFO @ Sun, 21 Jun 2020 16:36:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.05_model.r WARNING @ Sun, 21 Jun 2020 16:36:01: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:36:01: #2 You may need to consider one of the other alternative d(s): 4,46,592 WARNING @ Sun, 21 Jun 2020 16:36:01: #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 16:36:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:36:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:36:06: 2000000 INFO @ Sun, 21 Jun 2020 16:36:10: 3000000 INFO @ Sun, 21 Jun 2020 16:36:15: 4000000 INFO @ Sun, 21 Jun 2020 16:36:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:36:19: 5000000 INFO @ Sun, 21 Jun 2020 16:36:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:36:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:36:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.05_summits.bed INFO @ Sun, 21 Jun 2020 16:36:23: Done! pass1 - making usageList (895 chroms): 2 millis pass2 - checking and writing primary data (4112 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:36:24: 6000000 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 16:36:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.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 16:36:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:36:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:36:27: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:36:27: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:36:27: #1 total tags in treatment: 6693007 INFO @ Sun, 21 Jun 2020 16:36:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:36:27: #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 16:36:28: #1 tags after filtering in treatment: 6692990 INFO @ Sun, 21 Jun 2020 16:36:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:36:28: #1 finished! INFO @ Sun, 21 Jun 2020 16:36:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:36:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:36:28: #2 number of paired peaks: 2367 INFO @ Sun, 21 Jun 2020 16:36:28: start model_add_line... INFO @ Sun, 21 Jun 2020 16:36:28: start X-correlation... INFO @ Sun, 21 Jun 2020 16:36:28: end of X-cor INFO @ Sun, 21 Jun 2020 16:36:28: #2 finished! INFO @ Sun, 21 Jun 2020 16:36:28: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 16:36:28: #2 alternative fragment length(s) may be 4,46,592 bps INFO @ Sun, 21 Jun 2020 16:36:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.10_model.r WARNING @ Sun, 21 Jun 2020 16:36:28: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:36:28: #2 You may need to consider one of the other alternative d(s): 4,46,592 WARNING @ Sun, 21 Jun 2020 16:36:28: #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 16:36:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:36:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:36:31: 1000000 INFO @ Sun, 21 Jun 2020 16:36:35: 2000000 INFO @ Sun, 21 Jun 2020 16:36:40: 3000000 INFO @ Sun, 21 Jun 2020 16:36:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:36:44: 4000000 INFO @ Sun, 21 Jun 2020 16:36:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:36:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:36:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.10_summits.bed INFO @ Sun, 21 Jun 2020 16:36:49: Done! pass1 - making usageList (576 chroms): 1 millis pass2 - checking and writing primary data (1594 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:36:49: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:36:54: 6000000 INFO @ Sun, 21 Jun 2020 16:36:57: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:36:57: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:36:57: #1 total tags in treatment: 6693007 INFO @ Sun, 21 Jun 2020 16:36:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:36:57: #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 16:36:58: #1 tags after filtering in treatment: 6692990 INFO @ Sun, 21 Jun 2020 16:36:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:36:58: #1 finished! INFO @ Sun, 21 Jun 2020 16:36:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:36:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:36:58: #2 number of paired peaks: 2367 INFO @ Sun, 21 Jun 2020 16:36:58: start model_add_line... INFO @ Sun, 21 Jun 2020 16:36:58: start X-correlation... INFO @ Sun, 21 Jun 2020 16:36:58: end of X-cor INFO @ Sun, 21 Jun 2020 16:36:58: #2 finished! INFO @ Sun, 21 Jun 2020 16:36:58: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 16:36:58: #2 alternative fragment length(s) may be 4,46,592 bps INFO @ Sun, 21 Jun 2020 16:36:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.20_model.r WARNING @ Sun, 21 Jun 2020 16:36:58: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:36:58: #2 You may need to consider one of the other alternative d(s): 4,46,592 WARNING @ Sun, 21 Jun 2020 16:36:58: #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 16:36:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:36:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:37:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:37:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:37:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:37:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013101/SRX013101.20_summits.bed INFO @ Sun, 21 Jun 2020 16:37:19: Done! pass1 - making usageList (217 chroms): 1 millis pass2 - checking and writing primary data (456 records, 4 fields): 7 millis CompletedMACS2peakCalling