Job ID = 6452759 SRX = SRX030963 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:51:01 prefetch.2.10.7: 1) Downloading 'SRR072392'... 2020-06-21T07:51:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:55:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:55:09 prefetch.2.10.7: 'SRR072392' is valid 2020-06-21T07:55:09 prefetch.2.10.7: 1) 'SRR072392' was downloaded successfully Read 21965946 spots for SRR072392/SRR072392.sra Written 21965946 spots for SRR072392/SRR072392.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: 00:04:04 21965946 reads; of these: 21965946 (100.00%) were unpaired; of these: 2364832 (10.77%) aligned 0 times 15642784 (71.21%) aligned exactly 1 time 3958330 (18.02%) aligned >1 times 89.23% overall alignment rate Time searching: 00:04:04 Overall time: 00:04:04 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] 2112983 / 19601114 = 0.1078 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 17:04:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.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 17:04:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:04:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:04:48: 1000000 INFO @ Sun, 21 Jun 2020 17:04:55: 2000000 INFO @ Sun, 21 Jun 2020 17:05:01: 3000000 INFO @ Sun, 21 Jun 2020 17:05:08: 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 17:05:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.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 17:05:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:05:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:05:16: 5000000 INFO @ Sun, 21 Jun 2020 17:05:18: 1000000 INFO @ Sun, 21 Jun 2020 17:05:24: 6000000 INFO @ Sun, 21 Jun 2020 17:05:25: 2000000 INFO @ Sun, 21 Jun 2020 17:05:31: 7000000 INFO @ Sun, 21 Jun 2020 17:05:32: 3000000 INFO @ Sun, 21 Jun 2020 17:05:39: 8000000 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 17:05:39: 4000000 INFO @ Sun, 21 Jun 2020 17:05:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.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 17:05:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:05:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:05:47: 5000000 INFO @ Sun, 21 Jun 2020 17:05:47: 9000000 INFO @ Sun, 21 Jun 2020 17:05:50: 1000000 INFO @ Sun, 21 Jun 2020 17:05:54: 6000000 INFO @ Sun, 21 Jun 2020 17:05:55: 10000000 INFO @ Sun, 21 Jun 2020 17:05:57: 2000000 INFO @ Sun, 21 Jun 2020 17:06:01: 7000000 INFO @ Sun, 21 Jun 2020 17:06:03: 11000000 INFO @ Sun, 21 Jun 2020 17:06:04: 3000000 INFO @ Sun, 21 Jun 2020 17:06:08: 8000000 INFO @ Sun, 21 Jun 2020 17:06:11: 12000000 INFO @ Sun, 21 Jun 2020 17:06:11: 4000000 INFO @ Sun, 21 Jun 2020 17:06:16: 9000000 INFO @ Sun, 21 Jun 2020 17:06:19: 13000000 INFO @ Sun, 21 Jun 2020 17:06:19: 5000000 INFO @ Sun, 21 Jun 2020 17:06:23: 10000000 INFO @ Sun, 21 Jun 2020 17:06:26: 6000000 INFO @ Sun, 21 Jun 2020 17:06:27: 14000000 INFO @ Sun, 21 Jun 2020 17:06:31: 11000000 INFO @ Sun, 21 Jun 2020 17:06:34: 7000000 INFO @ Sun, 21 Jun 2020 17:06:35: 15000000 INFO @ Sun, 21 Jun 2020 17:06:38: 12000000 INFO @ Sun, 21 Jun 2020 17:06:41: 8000000 INFO @ Sun, 21 Jun 2020 17:06:43: 16000000 INFO @ Sun, 21 Jun 2020 17:06:46: 13000000 INFO @ Sun, 21 Jun 2020 17:06:49: 9000000 INFO @ Sun, 21 Jun 2020 17:06:52: 17000000 INFO @ Sun, 21 Jun 2020 17:06:53: 14000000 INFO @ Sun, 21 Jun 2020 17:06:56: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:06:56: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:06:56: #1 total tags in treatment: 17488131 INFO @ Sun, 21 Jun 2020 17:06:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:06:56: #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 17:06:56: 10000000 INFO @ Sun, 21 Jun 2020 17:06:56: #1 tags after filtering in treatment: 17488130 INFO @ Sun, 21 Jun 2020 17:06:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:06:56: #1 finished! INFO @ Sun, 21 Jun 2020 17:06:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:06:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:06:57: #2 number of paired peaks: 105 WARNING @ Sun, 21 Jun 2020 17:06:57: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Sun, 21 Jun 2020 17:06:57: start model_add_line... INFO @ Sun, 21 Jun 2020 17:06:57: start X-correlation... INFO @ Sun, 21 Jun 2020 17:06:57: end of X-cor INFO @ Sun, 21 Jun 2020 17:06:57: #2 finished! INFO @ Sun, 21 Jun 2020 17:06:57: #2 predicted fragment length is 70 bps INFO @ Sun, 21 Jun 2020 17:06:57: #2 alternative fragment length(s) may be 56,70,554 bps INFO @ Sun, 21 Jun 2020 17:06:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.05_model.r WARNING @ Sun, 21 Jun 2020 17:06:57: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:06:57: #2 You may need to consider one of the other alternative d(s): 56,70,554 WARNING @ Sun, 21 Jun 2020 17:06:57: #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 17:06:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:06:57: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:07:00: 15000000 INFO @ Sun, 21 Jun 2020 17:07:03: 11000000 INFO @ Sun, 21 Jun 2020 17:07:07: 16000000 INFO @ Sun, 21 Jun 2020 17:07:10: 12000000 INFO @ Sun, 21 Jun 2020 17:07:14: 17000000 INFO @ Sun, 21 Jun 2020 17:07:17: 13000000 INFO @ Sun, 21 Jun 2020 17:07:18: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:07:18: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:07:18: #1 total tags in treatment: 17488131 INFO @ Sun, 21 Jun 2020 17:07:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:07:18: #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 17:07:18: #1 tags after filtering in treatment: 17488130 INFO @ Sun, 21 Jun 2020 17:07:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:07:18: #1 finished! INFO @ Sun, 21 Jun 2020 17:07:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:07:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:07:19: #2 number of paired peaks: 105 WARNING @ Sun, 21 Jun 2020 17:07:19: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Sun, 21 Jun 2020 17:07:19: start model_add_line... INFO @ Sun, 21 Jun 2020 17:07:19: start X-correlation... INFO @ Sun, 21 Jun 2020 17:07:19: end of X-cor INFO @ Sun, 21 Jun 2020 17:07:19: #2 finished! INFO @ Sun, 21 Jun 2020 17:07:19: #2 predicted fragment length is 70 bps INFO @ Sun, 21 Jun 2020 17:07:19: #2 alternative fragment length(s) may be 56,70,554 bps INFO @ Sun, 21 Jun 2020 17:07:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.10_model.r WARNING @ Sun, 21 Jun 2020 17:07:19: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:07:19: #2 You may need to consider one of the other alternative d(s): 56,70,554 WARNING @ Sun, 21 Jun 2020 17:07:19: #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 17:07:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:07:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:07:23: 14000000 INFO @ Sun, 21 Jun 2020 17:07:30: 15000000 INFO @ Sun, 21 Jun 2020 17:07:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:07:35: 16000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:07:41: 17000000 INFO @ Sun, 21 Jun 2020 17:07:44: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:07:44: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:07:44: #1 total tags in treatment: 17488131 INFO @ Sun, 21 Jun 2020 17:07:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:07:44: #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 17:07:45: #1 tags after filtering in treatment: 17488130 INFO @ Sun, 21 Jun 2020 17:07:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:07:45: #1 finished! INFO @ Sun, 21 Jun 2020 17:07:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:07:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:07:46: #2 number of paired peaks: 105 WARNING @ Sun, 21 Jun 2020 17:07:46: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Sun, 21 Jun 2020 17:07:46: start model_add_line... INFO @ Sun, 21 Jun 2020 17:07:46: start X-correlation... INFO @ Sun, 21 Jun 2020 17:07:46: end of X-cor INFO @ Sun, 21 Jun 2020 17:07:46: #2 finished! INFO @ Sun, 21 Jun 2020 17:07:46: #2 predicted fragment length is 70 bps INFO @ Sun, 21 Jun 2020 17:07:46: #2 alternative fragment length(s) may be 56,70,554 bps INFO @ Sun, 21 Jun 2020 17:07:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.20_model.r WARNING @ Sun, 21 Jun 2020 17:07:46: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:07:46: #2 You may need to consider one of the other alternative d(s): 56,70,554 WARNING @ Sun, 21 Jun 2020 17:07:46: #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 17:07:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:07:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:07:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:07:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:07:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.05_summits.bed INFO @ Sun, 21 Jun 2020 17:07:50: Done! pass1 - making usageList (407 chroms): 2 millis pass2 - checking and writing primary data (1251 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:07:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:08:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:08:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:08:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.10_summits.bed INFO @ Sun, 21 Jun 2020 17:08:12: Done! pass1 - making usageList (184 chroms): 1 millis pass2 - checking and writing primary data (381 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:08:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:08:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:08:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:08:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX030963/SRX030963.20_summits.bed INFO @ Sun, 21 Jun 2020 17:08:39: Done! pass1 - making usageList (75 chroms): 1 millis pass2 - checking and writing primary data (154 records, 4 fields): 4 millis CompletedMACS2peakCalling