Job ID = 6458435 SRX = SRX5226989 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:30:19 prefetch.2.10.7: 1) Downloading 'SRR8417904'... 2020-06-21T12:30:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:34:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:34:31 prefetch.2.10.7: 1) 'SRR8417904' was downloaded successfully 2020-06-21T12:34:31 prefetch.2.10.7: 'SRR8417904' has 0 unresolved dependencies Read 20671478 spots for SRR8417904/SRR8417904.sra Written 20671478 spots for SRR8417904/SRR8417904.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: 00:07:02 20671478 reads; of these: 20671478 (100.00%) were unpaired; of these: 1056384 (5.11%) aligned 0 times 14598319 (70.62%) aligned exactly 1 time 5016775 (24.27%) aligned >1 times 94.89% overall alignment rate Time searching: 00:07:02 Overall time: 00:07:02 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] 2418004 / 19615094 = 0.1233 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 21:48:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.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 21:48:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:48:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:49:04: 1000000 INFO @ Sun, 21 Jun 2020 21:49:10: 2000000 INFO @ Sun, 21 Jun 2020 21:49:16: 3000000 INFO @ Sun, 21 Jun 2020 21:49:22: 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 21:49:28: 5000000 INFO @ Sun, 21 Jun 2020 21:49:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.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 21:49:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:49:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:49:34: 6000000 INFO @ Sun, 21 Jun 2020 21:49:35: 1000000 INFO @ Sun, 21 Jun 2020 21:49:41: 7000000 INFO @ Sun, 21 Jun 2020 21:49:41: 2000000 INFO @ Sun, 21 Jun 2020 21:49:47: 8000000 INFO @ Sun, 21 Jun 2020 21:49:48: 3000000 INFO @ Sun, 21 Jun 2020 21:49:54: 9000000 INFO @ Sun, 21 Jun 2020 21:49:54: 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 21:49:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.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 21:49:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:49:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:50:00: 10000000 INFO @ Sun, 21 Jun 2020 21:50:00: 5000000 INFO @ Sun, 21 Jun 2020 21:50:05: 1000000 INFO @ Sun, 21 Jun 2020 21:50:07: 11000000 INFO @ Sun, 21 Jun 2020 21:50:07: 6000000 INFO @ Sun, 21 Jun 2020 21:50:11: 2000000 INFO @ Sun, 21 Jun 2020 21:50:13: 12000000 INFO @ Sun, 21 Jun 2020 21:50:13: 7000000 INFO @ Sun, 21 Jun 2020 21:50:17: 3000000 INFO @ Sun, 21 Jun 2020 21:50:19: 13000000 INFO @ Sun, 21 Jun 2020 21:50:20: 8000000 INFO @ Sun, 21 Jun 2020 21:50:24: 4000000 INFO @ Sun, 21 Jun 2020 21:50:26: 14000000 INFO @ Sun, 21 Jun 2020 21:50:26: 9000000 INFO @ Sun, 21 Jun 2020 21:50:30: 5000000 INFO @ Sun, 21 Jun 2020 21:50:32: 15000000 INFO @ Sun, 21 Jun 2020 21:50:33: 10000000 INFO @ Sun, 21 Jun 2020 21:50:36: 6000000 INFO @ Sun, 21 Jun 2020 21:50:39: 16000000 INFO @ Sun, 21 Jun 2020 21:50:39: 11000000 INFO @ Sun, 21 Jun 2020 21:50:43: 7000000 INFO @ Sun, 21 Jun 2020 21:50:46: 12000000 INFO @ Sun, 21 Jun 2020 21:50:46: 17000000 INFO @ Sun, 21 Jun 2020 21:50:48: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:50:48: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:50:48: #1 total tags in treatment: 17197090 INFO @ Sun, 21 Jun 2020 21:50:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:50:48: #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 21:50:48: #1 tags after filtering in treatment: 17196960 INFO @ Sun, 21 Jun 2020 21:50:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:50:48: #1 finished! INFO @ Sun, 21 Jun 2020 21:50:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:50:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:50:50: #2 number of paired peaks: 901 WARNING @ Sun, 21 Jun 2020 21:50:50: Fewer paired peaks (901) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 901 pairs to build model! INFO @ Sun, 21 Jun 2020 21:50:50: start model_add_line... INFO @ Sun, 21 Jun 2020 21:50:50: 8000000 INFO @ Sun, 21 Jun 2020 21:50:50: start X-correlation... INFO @ Sun, 21 Jun 2020 21:50:50: end of X-cor INFO @ Sun, 21 Jun 2020 21:50:50: #2 finished! INFO @ Sun, 21 Jun 2020 21:50:50: #2 predicted fragment length is 101 bps INFO @ Sun, 21 Jun 2020 21:50:50: #2 alternative fragment length(s) may be 4,101 bps INFO @ Sun, 21 Jun 2020 21:50:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.05_model.r WARNING @ Sun, 21 Jun 2020 21:50:50: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:50:50: #2 You may need to consider one of the other alternative d(s): 4,101 WARNING @ Sun, 21 Jun 2020 21:50:50: #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 21:50:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:50:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:50:52: 13000000 INFO @ Sun, 21 Jun 2020 21:50:56: 9000000 INFO @ Sun, 21 Jun 2020 21:50:59: 14000000 INFO @ Sun, 21 Jun 2020 21:51:02: 10000000 INFO @ Sun, 21 Jun 2020 21:51:05: 15000000 INFO @ Sun, 21 Jun 2020 21:51:09: 11000000 INFO @ Sun, 21 Jun 2020 21:51:11: 16000000 INFO @ Sun, 21 Jun 2020 21:51:15: 12000000 INFO @ Sun, 21 Jun 2020 21:51:18: 17000000 INFO @ Sun, 21 Jun 2020 21:51:19: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:51:19: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:51:19: #1 total tags in treatment: 17197090 INFO @ Sun, 21 Jun 2020 21:51:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:51:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:51:20: #1 tags after filtering in treatment: 17196960 INFO @ Sun, 21 Jun 2020 21:51:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:51:20: #1 finished! INFO @ Sun, 21 Jun 2020 21:51:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:51:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:51:21: #2 number of paired peaks: 901 WARNING @ Sun, 21 Jun 2020 21:51:21: Fewer paired peaks (901) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 901 pairs to build model! INFO @ Sun, 21 Jun 2020 21:51:21: start model_add_line... INFO @ Sun, 21 Jun 2020 21:51:21: start X-correlation... INFO @ Sun, 21 Jun 2020 21:51:21: end of X-cor INFO @ Sun, 21 Jun 2020 21:51:21: #2 finished! INFO @ Sun, 21 Jun 2020 21:51:21: #2 predicted fragment length is 101 bps INFO @ Sun, 21 Jun 2020 21:51:21: #2 alternative fragment length(s) may be 4,101 bps INFO @ Sun, 21 Jun 2020 21:51:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.10_model.r WARNING @ Sun, 21 Jun 2020 21:51:21: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:51:21: #2 You may need to consider one of the other alternative d(s): 4,101 WARNING @ Sun, 21 Jun 2020 21:51:21: #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 21:51:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:51:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:51:21: 13000000 INFO @ Sun, 21 Jun 2020 21:51:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:51:27: 14000000 INFO @ Sun, 21 Jun 2020 21:51:33: 15000000 INFO @ Sun, 21 Jun 2020 21:51:39: 16000000 INFO @ Sun, 21 Jun 2020 21:51:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:51:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:51:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.05_summits.bed INFO @ Sun, 21 Jun 2020 21:51:40: Done! pass1 - making usageList (459 chroms): 1 millis pass2 - checking and writing primary data (6490 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:51:45: 17000000 INFO @ Sun, 21 Jun 2020 21:51:46: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:51:46: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:51:46: #1 total tags in treatment: 17197090 INFO @ Sun, 21 Jun 2020 21:51:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:51:46: #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 21:51:47: #1 tags after filtering in treatment: 17196960 INFO @ Sun, 21 Jun 2020 21:51:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:51:47: #1 finished! INFO @ Sun, 21 Jun 2020 21:51:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:51:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:51:48: #2 number of paired peaks: 901 WARNING @ Sun, 21 Jun 2020 21:51:48: Fewer paired peaks (901) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 901 pairs to build model! INFO @ Sun, 21 Jun 2020 21:51:48: start model_add_line... INFO @ Sun, 21 Jun 2020 21:51:48: start X-correlation... INFO @ Sun, 21 Jun 2020 21:51:48: end of X-cor INFO @ Sun, 21 Jun 2020 21:51:48: #2 finished! INFO @ Sun, 21 Jun 2020 21:51:48: #2 predicted fragment length is 101 bps INFO @ Sun, 21 Jun 2020 21:51:48: #2 alternative fragment length(s) may be 4,101 bps INFO @ Sun, 21 Jun 2020 21:51:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.20_model.r WARNING @ Sun, 21 Jun 2020 21:51:48: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:51:48: #2 You may need to consider one of the other alternative d(s): 4,101 WARNING @ Sun, 21 Jun 2020 21:51:48: #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 21:51:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:51:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:51:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:52:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:52:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:52:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.10_summits.bed INFO @ Sun, 21 Jun 2020 21:52:15: Done! pass1 - making usageList (394 chroms): 2 millis pass2 - checking and writing primary data (2863 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:52:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:52:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:52:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:52:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226989/SRX5226989.20_summits.bed INFO @ Sun, 21 Jun 2020 21:52:42: Done! pass1 - making usageList (275 chroms): 1 millis pass2 - checking and writing primary data (1119 records, 4 fields): 9 millis CompletedMACS2peakCalling