Job ID = 6454749 SRX = SRX2564134 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:27:44 prefetch.2.10.7: 1) Downloading 'SRR5259253'... 2020-06-21T09:27:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:35:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:35:19 prefetch.2.10.7: 1) 'SRR5259253' was downloaded successfully 2020-06-21T09:35:19 prefetch.2.10.7: 'SRR5259253' has 0 unresolved dependencies Read 44733354 spots for SRR5259253/SRR5259253.sra Written 44733354 spots for SRR5259253/SRR5259253.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: 00:15:18 44733354 reads; of these: 44733354 (100.00%) were unpaired; of these: 2032423 (4.54%) aligned 0 times 35508295 (79.38%) aligned exactly 1 time 7192636 (16.08%) aligned >1 times 95.46% overall alignment rate Time searching: 00:15:18 Overall time: 00:15:18 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 20 files... [bam_rmdupse_core] 14439261 / 42700931 = 0.3381 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 19:03:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.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 19:03:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:03:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:03:28: 1000000 INFO @ Sun, 21 Jun 2020 19:03:34: 2000000 INFO @ Sun, 21 Jun 2020 19:03:40: 3000000 INFO @ Sun, 21 Jun 2020 19:03:46: 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 19:03:52: 5000000 INFO @ Sun, 21 Jun 2020 19:03:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.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 19:03:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:03:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:03:59: 6000000 INFO @ Sun, 21 Jun 2020 19:03:59: 1000000 INFO @ Sun, 21 Jun 2020 19:04:05: 7000000 INFO @ Sun, 21 Jun 2020 19:04:06: 2000000 INFO @ Sun, 21 Jun 2020 19:04:12: 8000000 INFO @ Sun, 21 Jun 2020 19:04:12: 3000000 INFO @ Sun, 21 Jun 2020 19:04:18: 9000000 INFO @ Sun, 21 Jun 2020 19:04:19: 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 19:04:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.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 19:04:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:04:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:04:25: 10000000 INFO @ Sun, 21 Jun 2020 19:04:26: 5000000 INFO @ Sun, 21 Jun 2020 19:04:29: 1000000 INFO @ Sun, 21 Jun 2020 19:04:31: 11000000 INFO @ Sun, 21 Jun 2020 19:04:32: 6000000 INFO @ Sun, 21 Jun 2020 19:04:36: 2000000 INFO @ Sun, 21 Jun 2020 19:04:38: 12000000 INFO @ Sun, 21 Jun 2020 19:04:39: 7000000 INFO @ Sun, 21 Jun 2020 19:04:42: 3000000 INFO @ Sun, 21 Jun 2020 19:04:44: 13000000 INFO @ Sun, 21 Jun 2020 19:04:46: 8000000 INFO @ Sun, 21 Jun 2020 19:04:49: 4000000 INFO @ Sun, 21 Jun 2020 19:04:51: 14000000 INFO @ Sun, 21 Jun 2020 19:04:52: 9000000 INFO @ Sun, 21 Jun 2020 19:04:56: 5000000 INFO @ Sun, 21 Jun 2020 19:04:57: 15000000 INFO @ Sun, 21 Jun 2020 19:04:59: 10000000 INFO @ Sun, 21 Jun 2020 19:05:02: 6000000 INFO @ Sun, 21 Jun 2020 19:05:04: 16000000 INFO @ Sun, 21 Jun 2020 19:05:06: 11000000 INFO @ Sun, 21 Jun 2020 19:05:09: 7000000 INFO @ Sun, 21 Jun 2020 19:05:11: 17000000 INFO @ Sun, 21 Jun 2020 19:05:12: 12000000 INFO @ Sun, 21 Jun 2020 19:05:15: 8000000 INFO @ Sun, 21 Jun 2020 19:05:17: 18000000 INFO @ Sun, 21 Jun 2020 19:05:19: 13000000 INFO @ Sun, 21 Jun 2020 19:05:22: 9000000 INFO @ Sun, 21 Jun 2020 19:05:24: 19000000 INFO @ Sun, 21 Jun 2020 19:05:25: 14000000 INFO @ Sun, 21 Jun 2020 19:05:29: 10000000 INFO @ Sun, 21 Jun 2020 19:05:30: 20000000 INFO @ Sun, 21 Jun 2020 19:05:32: 15000000 INFO @ Sun, 21 Jun 2020 19:05:35: 11000000 INFO @ Sun, 21 Jun 2020 19:05:37: 21000000 INFO @ Sun, 21 Jun 2020 19:05:38: 16000000 INFO @ Sun, 21 Jun 2020 19:05:42: 12000000 INFO @ Sun, 21 Jun 2020 19:05:44: 22000000 INFO @ Sun, 21 Jun 2020 19:05:45: 17000000 INFO @ Sun, 21 Jun 2020 19:05:49: 13000000 INFO @ Sun, 21 Jun 2020 19:05:51: 23000000 INFO @ Sun, 21 Jun 2020 19:05:52: 18000000 INFO @ Sun, 21 Jun 2020 19:05:55: 14000000 INFO @ Sun, 21 Jun 2020 19:05:58: 24000000 INFO @ Sun, 21 Jun 2020 19:05:58: 19000000 INFO @ Sun, 21 Jun 2020 19:06:02: 15000000 INFO @ Sun, 21 Jun 2020 19:06:04: 25000000 INFO @ Sun, 21 Jun 2020 19:06:05: 20000000 INFO @ Sun, 21 Jun 2020 19:06:08: 16000000 INFO @ Sun, 21 Jun 2020 19:06:11: 26000000 INFO @ Sun, 21 Jun 2020 19:06:12: 21000000 INFO @ Sun, 21 Jun 2020 19:06:15: 17000000 INFO @ Sun, 21 Jun 2020 19:06:18: 27000000 INFO @ Sun, 21 Jun 2020 19:06:18: 22000000 INFO @ Sun, 21 Jun 2020 19:06:22: 18000000 INFO @ Sun, 21 Jun 2020 19:06:25: 28000000 INFO @ Sun, 21 Jun 2020 19:06:25: 23000000 INFO @ Sun, 21 Jun 2020 19:06:27: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 19:06:27: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 19:06:27: #1 total tags in treatment: 28261670 INFO @ Sun, 21 Jun 2020 19:06:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:06:27: #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 19:06:27: #1 tags after filtering in treatment: 28261670 INFO @ Sun, 21 Jun 2020 19:06:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:06:27: #1 finished! INFO @ Sun, 21 Jun 2020 19:06:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:06:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:06:28: 19000000 INFO @ Sun, 21 Jun 2020 19:06:29: #2 number of paired peaks: 582 WARNING @ Sun, 21 Jun 2020 19:06:29: Fewer paired peaks (582) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 582 pairs to build model! INFO @ Sun, 21 Jun 2020 19:06:29: start model_add_line... INFO @ Sun, 21 Jun 2020 19:06:30: start X-correlation... INFO @ Sun, 21 Jun 2020 19:06:30: end of X-cor INFO @ Sun, 21 Jun 2020 19:06:30: #2 finished! INFO @ Sun, 21 Jun 2020 19:06:30: #2 predicted fragment length is 133 bps INFO @ Sun, 21 Jun 2020 19:06:30: #2 alternative fragment length(s) may be 133 bps INFO @ Sun, 21 Jun 2020 19:06:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.05_model.r WARNING @ Sun, 21 Jun 2020 19:06:30: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:06:30: #2 You may need to consider one of the other alternative d(s): 133 WARNING @ Sun, 21 Jun 2020 19:06:30: #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 19:06:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:06:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:06:32: 24000000 INFO @ Sun, 21 Jun 2020 19:06:35: 20000000 INFO @ Sun, 21 Jun 2020 19:06:39: 25000000 INFO @ Sun, 21 Jun 2020 19:06:42: 21000000 INFO @ Sun, 21 Jun 2020 19:06:45: 26000000 INFO @ Sun, 21 Jun 2020 19:06:48: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:06:52: 27000000 INFO @ Sun, 21 Jun 2020 19:06:55: 23000000 INFO @ Sun, 21 Jun 2020 19:06:59: 28000000 INFO @ Sun, 21 Jun 2020 19:07:01: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 19:07:01: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 19:07:01: #1 total tags in treatment: 28261670 INFO @ Sun, 21 Jun 2020 19:07:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:07:01: #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 19:07:01: #1 tags after filtering in treatment: 28261670 INFO @ Sun, 21 Jun 2020 19:07:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:07:01: #1 finished! INFO @ Sun, 21 Jun 2020 19:07:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:07:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:07:02: 24000000 INFO @ Sun, 21 Jun 2020 19:07:03: #2 number of paired peaks: 582 WARNING @ Sun, 21 Jun 2020 19:07:03: Fewer paired peaks (582) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 582 pairs to build model! INFO @ Sun, 21 Jun 2020 19:07:03: start model_add_line... INFO @ Sun, 21 Jun 2020 19:07:03: start X-correlation... INFO @ Sun, 21 Jun 2020 19:07:03: end of X-cor INFO @ Sun, 21 Jun 2020 19:07:03: #2 finished! INFO @ Sun, 21 Jun 2020 19:07:03: #2 predicted fragment length is 133 bps INFO @ Sun, 21 Jun 2020 19:07:03: #2 alternative fragment length(s) may be 133 bps INFO @ Sun, 21 Jun 2020 19:07:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.10_model.r WARNING @ Sun, 21 Jun 2020 19:07:03: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:07:03: #2 You may need to consider one of the other alternative d(s): 133 WARNING @ Sun, 21 Jun 2020 19:07:03: #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 19:07:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:07:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:07:08: 25000000 INFO @ Sun, 21 Jun 2020 19:07:14: 26000000 INFO @ Sun, 21 Jun 2020 19:07:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:07:20: 27000000 INFO @ Sun, 21 Jun 2020 19:07:26: 28000000 INFO @ Sun, 21 Jun 2020 19:07:28: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 19:07:28: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 19:07:28: #1 total tags in treatment: 28261670 INFO @ Sun, 21 Jun 2020 19:07:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:07:28: #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 19:07:29: #1 tags after filtering in treatment: 28261670 INFO @ Sun, 21 Jun 2020 19:07:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:07:29: #1 finished! INFO @ Sun, 21 Jun 2020 19:07:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:07:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:07:31: #2 number of paired peaks: 582 WARNING @ Sun, 21 Jun 2020 19:07:31: Fewer paired peaks (582) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 582 pairs to build model! INFO @ Sun, 21 Jun 2020 19:07:31: start model_add_line... INFO @ Sun, 21 Jun 2020 19:07:31: start X-correlation... INFO @ Sun, 21 Jun 2020 19:07:31: end of X-cor INFO @ Sun, 21 Jun 2020 19:07:31: #2 finished! INFO @ Sun, 21 Jun 2020 19:07:31: #2 predicted fragment length is 133 bps INFO @ Sun, 21 Jun 2020 19:07:31: #2 alternative fragment length(s) may be 133 bps INFO @ Sun, 21 Jun 2020 19:07:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.20_model.r WARNING @ Sun, 21 Jun 2020 19:07:31: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:07:31: #2 You may need to consider one of the other alternative d(s): 133 WARNING @ Sun, 21 Jun 2020 19:07:31: #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 19:07:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:07:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:07:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:07:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:07:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.05_summits.bed INFO @ Sun, 21 Jun 2020 19:07:46: Done! pass1 - making usageList (646 chroms): 2 millis pass2 - checking and writing primary data (12707 records, 4 fields): 28 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:07:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:08:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:08:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:08:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.10_summits.bed INFO @ Sun, 21 Jun 2020 19:08:21: Done! pass1 - making usageList (541 chroms): 3 millis pass2 - checking and writing primary data (10560 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:08:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:08:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:08:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:08:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564134/SRX2564134.20_summits.bed INFO @ Sun, 21 Jun 2020 19:08:48: Done! pass1 - making usageList (452 chroms): 1 millis pass2 - checking and writing primary data (8430 records, 4 fields): 20 millis CompletedMACS2peakCalling