Job ID = 6456866 SRX = SRX403434 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:10:54 prefetch.2.10.7: 1) Downloading 'SRR1066649'... 2020-06-21T11:10:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:11:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:11:37 prefetch.2.10.7: 'SRR1066649' is valid 2020-06-21T11:11:37 prefetch.2.10.7: 1) 'SRR1066649' was downloaded successfully Read 6234913 spots for SRR1066649/SRR1066649.sra Written 6234913 spots for SRR1066649/SRR1066649.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: 00:01:25 6234913 reads; of these: 6234913 (100.00%) were unpaired; of these: 990273 (15.88%) aligned 0 times 3480577 (55.82%) aligned exactly 1 time 1764063 (28.29%) aligned >1 times 84.12% overall alignment rate Time searching: 00:01:25 Overall time: 00:01:25 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] 749977 / 5244640 = 0.1430 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 20:14:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.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 20:14:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:14:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:14:56: 1000000 INFO @ Sun, 21 Jun 2020 20:15:01: 2000000 INFO @ Sun, 21 Jun 2020 20:15:06: 3000000 INFO @ Sun, 21 Jun 2020 20:15:11: 4000000 INFO @ Sun, 21 Jun 2020 20:15:14: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:15:14: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:15:14: #1 total tags in treatment: 4494663 INFO @ Sun, 21 Jun 2020 20:15:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:15:14: #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 20:15:14: #1 tags after filtering in treatment: 4494653 INFO @ Sun, 21 Jun 2020 20:15:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:15:14: #1 finished! INFO @ Sun, 21 Jun 2020 20:15:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:15:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:15:15: #2 number of paired peaks: 1211 INFO @ Sun, 21 Jun 2020 20:15:15: start model_add_line... INFO @ Sun, 21 Jun 2020 20:15:15: start X-correlation... INFO @ Sun, 21 Jun 2020 20:15:15: end of X-cor INFO @ Sun, 21 Jun 2020 20:15:15: #2 finished! INFO @ Sun, 21 Jun 2020 20:15:15: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 20:15:15: #2 alternative fragment length(s) may be 4,45,86,595 bps INFO @ Sun, 21 Jun 2020 20:15:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.05_model.r WARNING @ Sun, 21 Jun 2020 20:15:15: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:15:15: #2 You may need to consider one of the other alternative d(s): 4,45,86,595 WARNING @ Sun, 21 Jun 2020 20:15:15: #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 20:15:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:15:15: #3 Pre-compute pvalue-qvalue table... 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 20:15:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.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 20:15:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:15:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:15:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:15:26: 1000000 INFO @ Sun, 21 Jun 2020 20:15:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:15:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:15:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.05_summits.bed INFO @ Sun, 21 Jun 2020 20:15:29: Done! pass1 - making usageList (471 chroms): 1 millis pass2 - checking and writing primary data (1381 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:15:31: 2000000 INFO @ Sun, 21 Jun 2020 20:15:36: 3000000 INFO @ Sun, 21 Jun 2020 20:15:42: 4000000 INFO @ Sun, 21 Jun 2020 20:15:44: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:15:44: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:15:44: #1 total tags in treatment: 4494663 INFO @ Sun, 21 Jun 2020 20:15:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:15:44: #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 20:15:45: #1 tags after filtering in treatment: 4494653 INFO @ Sun, 21 Jun 2020 20:15:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:15:45: #1 finished! INFO @ Sun, 21 Jun 2020 20:15:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:15:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:15:45: #2 number of paired peaks: 1211 INFO @ Sun, 21 Jun 2020 20:15:45: start model_add_line... INFO @ Sun, 21 Jun 2020 20:15:45: start X-correlation... INFO @ Sun, 21 Jun 2020 20:15:45: end of X-cor INFO @ Sun, 21 Jun 2020 20:15:45: #2 finished! INFO @ Sun, 21 Jun 2020 20:15:45: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 20:15:45: #2 alternative fragment length(s) may be 4,45,86,595 bps INFO @ Sun, 21 Jun 2020 20:15:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.10_model.r WARNING @ Sun, 21 Jun 2020 20:15:45: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:15:45: #2 You may need to consider one of the other alternative d(s): 4,45,86,595 WARNING @ Sun, 21 Jun 2020 20:15:45: #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 20:15:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:15:45: #3 Pre-compute pvalue-qvalue table... 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 20:15:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.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 20:15:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:15:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:15:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:15:56: 1000000 INFO @ Sun, 21 Jun 2020 20:16:01: 2000000 INFO @ Sun, 21 Jun 2020 20:16:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:16:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:16:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.10_summits.bed INFO @ Sun, 21 Jun 2020 20:16:01: Done! pass1 - making usageList (224 chroms): 0 millis pass2 - checking and writing primary data (464 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:16:06: 3000000 INFO @ Sun, 21 Jun 2020 20:16:11: 4000000 INFO @ Sun, 21 Jun 2020 20:16:14: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:16:14: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:16:14: #1 total tags in treatment: 4494663 INFO @ Sun, 21 Jun 2020 20:16:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:16:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:16:14: #1 tags after filtering in treatment: 4494653 INFO @ Sun, 21 Jun 2020 20:16:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:16:14: #1 finished! INFO @ Sun, 21 Jun 2020 20:16:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:16:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:16:15: #2 number of paired peaks: 1211 INFO @ Sun, 21 Jun 2020 20:16:15: start model_add_line... INFO @ Sun, 21 Jun 2020 20:16:15: start X-correlation... INFO @ Sun, 21 Jun 2020 20:16:15: end of X-cor INFO @ Sun, 21 Jun 2020 20:16:15: #2 finished! INFO @ Sun, 21 Jun 2020 20:16:15: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 20:16:15: #2 alternative fragment length(s) may be 4,45,86,595 bps INFO @ Sun, 21 Jun 2020 20:16:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.20_model.r WARNING @ Sun, 21 Jun 2020 20:16:15: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:16:15: #2 You may need to consider one of the other alternative d(s): 4,45,86,595 WARNING @ Sun, 21 Jun 2020 20:16:15: #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 20:16:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:16:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:16:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:16:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:16:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:16:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX403434/SRX403434.20_summits.bed INFO @ Sun, 21 Jun 2020 20:16:30: Done! pass1 - making usageList (83 chroms): 1 millis pass2 - checking and writing primary data (125 records, 4 fields): 4 millis CompletedMACS2peakCalling