Job ID = 6456664 SRX = SRX3937191 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:08:39 prefetch.2.10.7: 1) Downloading 'SRR7004611'... 2020-06-21T11:08:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:10:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:10:24 prefetch.2.10.7: 'SRR7004611' is valid 2020-06-21T11:10:24 prefetch.2.10.7: 1) 'SRR7004611' was downloaded successfully 2020-06-21T11:10:24 prefetch.2.10.7: 'SRR7004611' has 0 unresolved dependencies Read 3700347 spots for SRR7004611/SRR7004611.sra Written 3700347 spots for SRR7004611/SRR7004611.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: 00:01:37 3700347 reads; of these: 3700347 (100.00%) were unpaired; of these: 1007060 (27.22%) aligned 0 times 2040781 (55.15%) aligned exactly 1 time 652506 (17.63%) aligned >1 times 72.78% overall alignment rate Time searching: 00:01:37 Overall time: 00:01:37 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] 235891 / 2693287 = 0.0876 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 20:13:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.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 20:13:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:13:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:13:54: 1000000 INFO @ Sun, 21 Jun 2020 20:14:01: 2000000 INFO @ Sun, 21 Jun 2020 20:14:04: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 20:14:04: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 20:14:04: #1 total tags in treatment: 2457396 INFO @ Sun, 21 Jun 2020 20:14:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:14:04: #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 20:14:05: #1 tags after filtering in treatment: 2457326 INFO @ Sun, 21 Jun 2020 20:14:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:14:05: #1 finished! INFO @ Sun, 21 Jun 2020 20:14:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:14:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:14:05: #2 number of paired peaks: 1542 INFO @ Sun, 21 Jun 2020 20:14:05: start model_add_line... INFO @ Sun, 21 Jun 2020 20:14:05: start X-correlation... INFO @ Sun, 21 Jun 2020 20:14:05: end of X-cor INFO @ Sun, 21 Jun 2020 20:14:05: #2 finished! INFO @ Sun, 21 Jun 2020 20:14:05: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 20:14:05: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 21 Jun 2020 20:14:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.05_model.r WARNING @ Sun, 21 Jun 2020 20:14:05: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:14:05: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sun, 21 Jun 2020 20:14:05: #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 20:14:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:14:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:14:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:14:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:14:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:14:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.05_summits.bed INFO @ Sun, 21 Jun 2020 20:14:14: Done! pass1 - making usageList (359 chroms): 1 millis pass2 - checking and writing primary data (633 records, 4 fields): 12 millis CompletedMACS2peakCalling 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 20:14:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.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 20:14:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:14:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:14:24: 1000000 INFO @ Sun, 21 Jun 2020 20:14:31: 2000000 INFO @ Sun, 21 Jun 2020 20:14:35: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 20:14:35: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 20:14:35: #1 total tags in treatment: 2457396 INFO @ Sun, 21 Jun 2020 20:14:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:14:35: #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 20:14:35: #1 tags after filtering in treatment: 2457326 INFO @ Sun, 21 Jun 2020 20:14:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:14:35: #1 finished! INFO @ Sun, 21 Jun 2020 20:14:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:14:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:14:36: #2 number of paired peaks: 1542 INFO @ Sun, 21 Jun 2020 20:14:36: start model_add_line... INFO @ Sun, 21 Jun 2020 20:14:36: start X-correlation... INFO @ Sun, 21 Jun 2020 20:14:36: end of X-cor INFO @ Sun, 21 Jun 2020 20:14:36: #2 finished! INFO @ Sun, 21 Jun 2020 20:14:36: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 20:14:36: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 21 Jun 2020 20:14:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.10_model.r WARNING @ Sun, 21 Jun 2020 20:14:36: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:14:36: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sun, 21 Jun 2020 20:14:36: #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 20:14:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:14:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:14:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:14:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:14:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:14:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.10_summits.bed INFO @ Sun, 21 Jun 2020 20:14:45: Done! pass1 - making usageList (206 chroms): 0 millis pass2 - checking and writing primary data (331 records, 4 fields): 8 millis BedGraph に変換中... CompletedMACS2peakCalling 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 20:14:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.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 20:14:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:14:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:14:55: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:15:02: 2000000 INFO @ Sun, 21 Jun 2020 20:15:05: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 20:15:05: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 20:15:05: #1 total tags in treatment: 2457396 INFO @ Sun, 21 Jun 2020 20:15:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:15:05: #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 20:15:06: #1 tags after filtering in treatment: 2457326 INFO @ Sun, 21 Jun 2020 20:15:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:15:06: #1 finished! INFO @ Sun, 21 Jun 2020 20:15:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:15:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:15:06: #2 number of paired peaks: 1542 INFO @ Sun, 21 Jun 2020 20:15:06: start model_add_line... INFO @ Sun, 21 Jun 2020 20:15:06: start X-correlation... INFO @ Sun, 21 Jun 2020 20:15:06: end of X-cor INFO @ Sun, 21 Jun 2020 20:15:06: #2 finished! INFO @ Sun, 21 Jun 2020 20:15:06: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 20:15:06: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 21 Jun 2020 20:15:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.20_model.r WARNING @ Sun, 21 Jun 2020 20:15:06: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:15:06: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sun, 21 Jun 2020 20:15:06: #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 20:15:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:15:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:15:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:15:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:15:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:15:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3937191/SRX3937191.20_summits.bed INFO @ Sun, 21 Jun 2020 20:15:15: Done! pass1 - making usageList (118 chroms): 1 millis pass2 - checking and writing primary data (189 records, 4 fields): 4 millis CompletedMACS2peakCalling