Job ID = 6455707 SRX = SRX288007 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:14:36 prefetch.2.10.7: 1) Downloading 'SRR870196'... 2020-06-21T10:14:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:17:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:17:39 prefetch.2.10.7: 1) 'SRR870196' was downloaded successfully Read 17570684 spots for SRR870196/SRR870196.sra Written 17570684 spots for SRR870196/SRR870196.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: 00:05:21 17570684 reads; of these: 17570684 (100.00%) were unpaired; of these: 1164922 (6.63%) aligned 0 times 11092319 (63.13%) aligned exactly 1 time 5313443 (30.24%) aligned >1 times 93.37% overall alignment rate Time searching: 00:05:21 Overall time: 00:05:21 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_sort_core] merging from 8 files... [bam_rmdupse_core] 3298231 / 16405762 = 0.2010 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 19:28:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.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 19:28:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:28:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:28:08: 1000000 INFO @ Sun, 21 Jun 2020 19:28:13: 2000000 INFO @ Sun, 21 Jun 2020 19:28:19: 3000000 INFO @ Sun, 21 Jun 2020 19:28:25: 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 @ Sun, 21 Jun 2020 19:28:31: 5000000 INFO @ Sun, 21 Jun 2020 19:28:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.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 19:28:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:28:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:28:37: 6000000 INFO @ Sun, 21 Jun 2020 19:28:39: 1000000 INFO @ Sun, 21 Jun 2020 19:28:44: 7000000 INFO @ Sun, 21 Jun 2020 19:28:46: 2000000 INFO @ Sun, 21 Jun 2020 19:28:51: 8000000 INFO @ Sun, 21 Jun 2020 19:28:53: 3000000 INFO @ Sun, 21 Jun 2020 19:28:58: 9000000 INFO @ Sun, 21 Jun 2020 19:28:59: 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 @ Sun, 21 Jun 2020 19:29:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.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 19:29:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:29:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:29:04: 10000000 INFO @ Sun, 21 Jun 2020 19:29:06: 5000000 INFO @ Sun, 21 Jun 2020 19:29:11: 1000000 INFO @ Sun, 21 Jun 2020 19:29:11: 11000000 INFO @ Sun, 21 Jun 2020 19:29:13: 6000000 INFO @ Sun, 21 Jun 2020 19:29:18: 2000000 INFO @ Sun, 21 Jun 2020 19:29:18: 12000000 INFO @ Sun, 21 Jun 2020 19:29:20: 7000000 INFO @ Sun, 21 Jun 2020 19:29:24: 3000000 INFO @ Sun, 21 Jun 2020 19:29:25: 13000000 INFO @ Sun, 21 Jun 2020 19:29:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:29:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:29:26: #1 total tags in treatment: 13107531 INFO @ Sun, 21 Jun 2020 19:29:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:29:26: #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 19:29:26: #1 tags after filtering in treatment: 13107531 INFO @ Sun, 21 Jun 2020 19:29:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:29:26: #1 finished! INFO @ Sun, 21 Jun 2020 19:29:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:29:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:29:27: 8000000 INFO @ Sun, 21 Jun 2020 19:29:27: #2 number of paired peaks: 550 WARNING @ Sun, 21 Jun 2020 19:29:27: Fewer paired peaks (550) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 550 pairs to build model! INFO @ Sun, 21 Jun 2020 19:29:27: start model_add_line... INFO @ Sun, 21 Jun 2020 19:29:27: start X-correlation... INFO @ Sun, 21 Jun 2020 19:29:27: end of X-cor INFO @ Sun, 21 Jun 2020 19:29:27: #2 finished! INFO @ Sun, 21 Jun 2020 19:29:27: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:29:27: #2 alternative fragment length(s) may be 3,42,542 bps INFO @ Sun, 21 Jun 2020 19:29:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.05_model.r WARNING @ Sun, 21 Jun 2020 19:29:27: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:29:27: #2 You may need to consider one of the other alternative d(s): 3,42,542 WARNING @ Sun, 21 Jun 2020 19:29:27: #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 19:29:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:29:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:29:31: 4000000 INFO @ Sun, 21 Jun 2020 19:29:34: 9000000 INFO @ Sun, 21 Jun 2020 19:29:38: 5000000 INFO @ Sun, 21 Jun 2020 19:29:40: 10000000 INFO @ Sun, 21 Jun 2020 19:29:45: 6000000 INFO @ Sun, 21 Jun 2020 19:29:47: 11000000 INFO @ Sun, 21 Jun 2020 19:29:51: 7000000 INFO @ Sun, 21 Jun 2020 19:29:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:29:54: 12000000 INFO @ Sun, 21 Jun 2020 19:29:58: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:30:01: 13000000 INFO @ Sun, 21 Jun 2020 19:30:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:30:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:30:02: #1 total tags in treatment: 13107531 INFO @ Sun, 21 Jun 2020 19:30:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:30:02: #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 19:30:03: #1 tags after filtering in treatment: 13107531 INFO @ Sun, 21 Jun 2020 19:30:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:30:03: #1 finished! INFO @ Sun, 21 Jun 2020 19:30:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:30:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:30:04: #2 number of paired peaks: 550 WARNING @ Sun, 21 Jun 2020 19:30:04: Fewer paired peaks (550) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 550 pairs to build model! INFO @ Sun, 21 Jun 2020 19:30:04: start model_add_line... INFO @ Sun, 21 Jun 2020 19:30:04: start X-correlation... INFO @ Sun, 21 Jun 2020 19:30:04: end of X-cor INFO @ Sun, 21 Jun 2020 19:30:04: #2 finished! INFO @ Sun, 21 Jun 2020 19:30:04: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:30:04: #2 alternative fragment length(s) may be 3,42,542 bps INFO @ Sun, 21 Jun 2020 19:30:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.10_model.r WARNING @ Sun, 21 Jun 2020 19:30:04: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:30:04: #2 You may need to consider one of the other alternative d(s): 3,42,542 WARNING @ Sun, 21 Jun 2020 19:30:04: #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 19:30:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:30:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:30:05: 9000000 INFO @ Sun, 21 Jun 2020 19:30:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:30:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:30:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.05_summits.bed INFO @ Sun, 21 Jun 2020 19:30:05: Done! pass1 - making usageList (599 chroms): 1 millis pass2 - checking and writing primary data (2355 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:30:11: 10000000 INFO @ Sun, 21 Jun 2020 19:30:17: 11000000 INFO @ Sun, 21 Jun 2020 19:30:23: 12000000 INFO @ Sun, 21 Jun 2020 19:30:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:30:30: 13000000 INFO @ Sun, 21 Jun 2020 19:30:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:30:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:30:30: #1 total tags in treatment: 13107531 INFO @ Sun, 21 Jun 2020 19:30:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:30:30: #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 19:30:31: #1 tags after filtering in treatment: 13107531 INFO @ Sun, 21 Jun 2020 19:30:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:30:31: #1 finished! INFO @ Sun, 21 Jun 2020 19:30:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:30:31: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:30:32: #2 number of paired peaks: 550 WARNING @ Sun, 21 Jun 2020 19:30:32: Fewer paired peaks (550) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 550 pairs to build model! INFO @ Sun, 21 Jun 2020 19:30:32: start model_add_line... INFO @ Sun, 21 Jun 2020 19:30:32: start X-correlation... INFO @ Sun, 21 Jun 2020 19:30:32: end of X-cor INFO @ Sun, 21 Jun 2020 19:30:32: #2 finished! INFO @ Sun, 21 Jun 2020 19:30:32: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:30:32: #2 alternative fragment length(s) may be 3,42,542 bps INFO @ Sun, 21 Jun 2020 19:30:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.20_model.r WARNING @ Sun, 21 Jun 2020 19:30:32: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:30:32: #2 You may need to consider one of the other alternative d(s): 3,42,542 WARNING @ Sun, 21 Jun 2020 19:30:32: #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 19:30:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:30:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:30:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:30:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:30:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.10_summits.bed INFO @ Sun, 21 Jun 2020 19:30:41: Done! pass1 - making usageList (501 chroms): 1 millis pass2 - checking and writing primary data (1803 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:30:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:31:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:31:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:31:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288007/SRX288007.20_summits.bed INFO @ Sun, 21 Jun 2020 19:31:09: Done! pass1 - making usageList (291 chroms): 1 millis pass2 - checking and writing primary data (594 records, 4 fields): 9 millis CompletedMACS2peakCalling