Job ID = 6456930 SRX = SRX4158161 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:11:12 prefetch.2.10.7: 1) Downloading 'SRR7253441'... 2020-06-21T11:11:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:15:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:15:58 prefetch.2.10.7: 1) 'SRR7253441' was downloaded successfully Read 34237743 spots for SRR7253441/SRR7253441.sra Written 34237743 spots for SRR7253441/SRR7253441.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: 00:08:24 34237743 reads; of these: 34237743 (100.00%) were unpaired; of these: 2668258 (7.79%) aligned 0 times 27454400 (80.19%) aligned exactly 1 time 4115085 (12.02%) aligned >1 times 92.21% overall alignment rate Time searching: 00:08:24 Overall time: 00:08:24 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 16 files... [bam_rmdupse_core] 4876687 / 31569485 = 0.1545 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 20:33:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.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 20:33:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:33:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:33:54: 1000000 INFO @ Sun, 21 Jun 2020 20:34:00: 2000000 INFO @ Sun, 21 Jun 2020 20:34:06: 3000000 INFO @ Sun, 21 Jun 2020 20:34:12: 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 20:34:18: 5000000 INFO @ Sun, 21 Jun 2020 20:34:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.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 20:34:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:34:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:34:24: 6000000 INFO @ Sun, 21 Jun 2020 20:34:25: 1000000 INFO @ Sun, 21 Jun 2020 20:34:30: 7000000 INFO @ Sun, 21 Jun 2020 20:34:31: 2000000 INFO @ Sun, 21 Jun 2020 20:34:36: 8000000 INFO @ Sun, 21 Jun 2020 20:34:37: 3000000 INFO @ Sun, 21 Jun 2020 20:34:42: 9000000 INFO @ Sun, 21 Jun 2020 20:34:43: 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 20:34:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.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 20:34:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:34:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:34:48: 10000000 INFO @ Sun, 21 Jun 2020 20:34:49: 5000000 INFO @ Sun, 21 Jun 2020 20:34:55: 11000000 INFO @ Sun, 21 Jun 2020 20:34:55: 1000000 INFO @ Sun, 21 Jun 2020 20:34:55: 6000000 INFO @ Sun, 21 Jun 2020 20:35:01: 12000000 INFO @ Sun, 21 Jun 2020 20:35:01: 2000000 INFO @ Sun, 21 Jun 2020 20:35:01: 7000000 INFO @ Sun, 21 Jun 2020 20:35:07: 13000000 INFO @ Sun, 21 Jun 2020 20:35:07: 3000000 INFO @ Sun, 21 Jun 2020 20:35:07: 8000000 INFO @ Sun, 21 Jun 2020 20:35:13: 14000000 INFO @ Sun, 21 Jun 2020 20:35:13: 4000000 INFO @ Sun, 21 Jun 2020 20:35:13: 9000000 INFO @ Sun, 21 Jun 2020 20:35:19: 15000000 INFO @ Sun, 21 Jun 2020 20:35:19: 5000000 INFO @ Sun, 21 Jun 2020 20:35:20: 10000000 INFO @ Sun, 21 Jun 2020 20:35:25: 16000000 INFO @ Sun, 21 Jun 2020 20:35:26: 6000000 INFO @ Sun, 21 Jun 2020 20:35:26: 11000000 INFO @ Sun, 21 Jun 2020 20:35:32: 17000000 INFO @ Sun, 21 Jun 2020 20:35:32: 7000000 INFO @ Sun, 21 Jun 2020 20:35:32: 12000000 INFO @ Sun, 21 Jun 2020 20:35:38: 18000000 INFO @ Sun, 21 Jun 2020 20:35:38: 8000000 INFO @ Sun, 21 Jun 2020 20:35:38: 13000000 INFO @ Sun, 21 Jun 2020 20:35:44: 19000000 INFO @ Sun, 21 Jun 2020 20:35:44: 9000000 INFO @ Sun, 21 Jun 2020 20:35:44: 14000000 INFO @ Sun, 21 Jun 2020 20:35:50: 20000000 INFO @ Sun, 21 Jun 2020 20:35:50: 10000000 INFO @ Sun, 21 Jun 2020 20:35:51: 15000000 INFO @ Sun, 21 Jun 2020 20:35:56: 21000000 INFO @ Sun, 21 Jun 2020 20:35:57: 11000000 INFO @ Sun, 21 Jun 2020 20:35:57: 16000000 INFO @ Sun, 21 Jun 2020 20:36:02: 22000000 INFO @ Sun, 21 Jun 2020 20:36:03: 12000000 INFO @ Sun, 21 Jun 2020 20:36:03: 17000000 INFO @ Sun, 21 Jun 2020 20:36:09: 23000000 INFO @ Sun, 21 Jun 2020 20:36:09: 13000000 INFO @ Sun, 21 Jun 2020 20:36:09: 18000000 INFO @ Sun, 21 Jun 2020 20:36:14: 24000000 INFO @ Sun, 21 Jun 2020 20:36:15: 14000000 INFO @ Sun, 21 Jun 2020 20:36:15: 19000000 INFO @ Sun, 21 Jun 2020 20:36:21: 25000000 INFO @ Sun, 21 Jun 2020 20:36:21: 15000000 INFO @ Sun, 21 Jun 2020 20:36:21: 20000000 INFO @ Sun, 21 Jun 2020 20:36:26: 26000000 INFO @ Sun, 21 Jun 2020 20:36:27: 16000000 INFO @ Sun, 21 Jun 2020 20:36:28: 21000000 INFO @ Sun, 21 Jun 2020 20:36:31: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:36:31: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:36:31: #1 total tags in treatment: 26692798 INFO @ Sun, 21 Jun 2020 20:36:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:36:31: #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 20:36:32: #1 tags after filtering in treatment: 26692706 INFO @ Sun, 21 Jun 2020 20:36:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:36:32: #1 finished! INFO @ Sun, 21 Jun 2020 20:36:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:36:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:36:33: 17000000 INFO @ Sun, 21 Jun 2020 20:36:33: #2 number of paired peaks: 178 WARNING @ Sun, 21 Jun 2020 20:36:33: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sun, 21 Jun 2020 20:36:33: start model_add_line... INFO @ Sun, 21 Jun 2020 20:36:34: start X-correlation... INFO @ Sun, 21 Jun 2020 20:36:34: end of X-cor INFO @ Sun, 21 Jun 2020 20:36:34: #2 finished! INFO @ Sun, 21 Jun 2020 20:36:34: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 20:36:34: #2 alternative fragment length(s) may be 1,46,535,548,576 bps INFO @ Sun, 21 Jun 2020 20:36:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.05_model.r WARNING @ Sun, 21 Jun 2020 20:36:34: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:36:34: #2 You may need to consider one of the other alternative d(s): 1,46,535,548,576 WARNING @ Sun, 21 Jun 2020 20:36:34: #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 20:36:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:36:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:36:34: 22000000 INFO @ Sun, 21 Jun 2020 20:36:39: 18000000 INFO @ Sun, 21 Jun 2020 20:36:40: 23000000 INFO @ Sun, 21 Jun 2020 20:36:45: 19000000 INFO @ Sun, 21 Jun 2020 20:36:46: 24000000 INFO @ Sun, 21 Jun 2020 20:36:51: 20000000 INFO @ Sun, 21 Jun 2020 20:36:52: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:36:57: 21000000 INFO @ Sun, 21 Jun 2020 20:36:58: 26000000 INFO @ Sun, 21 Jun 2020 20:37:02: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:37:02: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:37:02: #1 total tags in treatment: 26692798 INFO @ Sun, 21 Jun 2020 20:37:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:37:02: #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 20:37:03: #1 tags after filtering in treatment: 26692706 INFO @ Sun, 21 Jun 2020 20:37:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:37:03: #1 finished! INFO @ Sun, 21 Jun 2020 20:37:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:37:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:37:03: 22000000 INFO @ Sun, 21 Jun 2020 20:37:05: #2 number of paired peaks: 178 WARNING @ Sun, 21 Jun 2020 20:37:05: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sun, 21 Jun 2020 20:37:05: start model_add_line... INFO @ Sun, 21 Jun 2020 20:37:05: start X-correlation... INFO @ Sun, 21 Jun 2020 20:37:05: end of X-cor INFO @ Sun, 21 Jun 2020 20:37:05: #2 finished! INFO @ Sun, 21 Jun 2020 20:37:05: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 20:37:05: #2 alternative fragment length(s) may be 1,46,535,548,576 bps INFO @ Sun, 21 Jun 2020 20:37:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.10_model.r WARNING @ Sun, 21 Jun 2020 20:37:05: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:37:05: #2 You may need to consider one of the other alternative d(s): 1,46,535,548,576 WARNING @ Sun, 21 Jun 2020 20:37:05: #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 20:37:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:37:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:37:09: 23000000 INFO @ Sun, 21 Jun 2020 20:37:14: 24000000 INFO @ Sun, 21 Jun 2020 20:37:20: 25000000 INFO @ Sun, 21 Jun 2020 20:37:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:37:26: 26000000 INFO @ Sun, 21 Jun 2020 20:37:30: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:37:30: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:37:30: #1 total tags in treatment: 26692798 INFO @ Sun, 21 Jun 2020 20:37:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:37:30: #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 20:37:31: #1 tags after filtering in treatment: 26692706 INFO @ Sun, 21 Jun 2020 20:37:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:37:31: #1 finished! INFO @ Sun, 21 Jun 2020 20:37:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:37:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:37:33: #2 number of paired peaks: 178 WARNING @ Sun, 21 Jun 2020 20:37:33: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sun, 21 Jun 2020 20:37:33: start model_add_line... INFO @ Sun, 21 Jun 2020 20:37:33: start X-correlation... INFO @ Sun, 21 Jun 2020 20:37:33: end of X-cor INFO @ Sun, 21 Jun 2020 20:37:33: #2 finished! INFO @ Sun, 21 Jun 2020 20:37:33: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 20:37:33: #2 alternative fragment length(s) may be 1,46,535,548,576 bps INFO @ Sun, 21 Jun 2020 20:37:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.20_model.r WARNING @ Sun, 21 Jun 2020 20:37:33: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:37:33: #2 You may need to consider one of the other alternative d(s): 1,46,535,548,576 WARNING @ Sun, 21 Jun 2020 20:37:33: #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 20:37:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:37:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:37:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:37:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:37:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.05_summits.bed INFO @ Sun, 21 Jun 2020 20:37:47: Done! pass1 - making usageList (132 chroms): 1 millis pass2 - checking and writing primary data (463 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:37:52: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:38:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:38:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:38:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.10_summits.bed INFO @ Sun, 21 Jun 2020 20:38:15: Done! pass1 - making usageList (108 chroms): 1 millis pass2 - checking and writing primary data (317 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:38:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:38:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:38:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:38:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158161/SRX4158161.20_summits.bed INFO @ Sun, 21 Jun 2020 20:38:44: Done! pass1 - making usageList (76 chroms): 0 millis pass2 - checking and writing primary data (200 records, 4 fields): 4 millis CompletedMACS2peakCalling