Job ID = 6453835 SRX = SRX152090 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:24:17 prefetch.2.10.7: 1) Downloading 'SRR504946'... 2020-06-21T08:24:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:33:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:33:55 prefetch.2.10.7: 1) 'SRR504946' was downloaded successfully Read 37981047 spots for SRR504946/SRR504946.sra Written 37981047 spots for SRR504946/SRR504946.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: 00:25:58 37981047 reads; of these: 37981047 (100.00%) were unpaired; of these: 2312865 (6.09%) aligned 0 times 16141953 (42.50%) aligned exactly 1 time 19526229 (51.41%) aligned >1 times 93.91% overall alignment rate Time searching: 00:25:58 Overall time: 00:25:58 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] 25077646 / 35668182 = 0.7031 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 18:10:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.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 18:10:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:10:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:10:30: 1000000 INFO @ Sun, 21 Jun 2020 18:10:36: 2000000 INFO @ Sun, 21 Jun 2020 18:10:42: 3000000 INFO @ Sun, 21 Jun 2020 18:10:49: 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 18:10:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.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 18:10:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:10:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:10:55: 5000000 INFO @ Sun, 21 Jun 2020 18:11:01: 1000000 INFO @ Sun, 21 Jun 2020 18:11:02: 6000000 INFO @ Sun, 21 Jun 2020 18:11:08: 7000000 INFO @ Sun, 21 Jun 2020 18:11:10: 2000000 INFO @ Sun, 21 Jun 2020 18:11:14: 8000000 INFO @ Sun, 21 Jun 2020 18:11:18: 3000000 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 18:11:22: 9000000 INFO @ Sun, 21 Jun 2020 18:11:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.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 18:11:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:11:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:11:26: 4000000 INFO @ Sun, 21 Jun 2020 18:11:29: 10000000 INFO @ Sun, 21 Jun 2020 18:11:31: 1000000 INFO @ Sun, 21 Jun 2020 18:11:34: 5000000 INFO @ Sun, 21 Jun 2020 18:11:34: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:11:34: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:11:34: #1 total tags in treatment: 10590536 INFO @ Sun, 21 Jun 2020 18:11:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:11:34: #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 18:11:35: #1 tags after filtering in treatment: 10590533 INFO @ Sun, 21 Jun 2020 18:11:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:11:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:11:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:11:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:11:36: #2 number of paired peaks: 2852 INFO @ Sun, 21 Jun 2020 18:11:36: start model_add_line... INFO @ Sun, 21 Jun 2020 18:11:36: start X-correlation... INFO @ Sun, 21 Jun 2020 18:11:36: end of X-cor INFO @ Sun, 21 Jun 2020 18:11:36: #2 finished! INFO @ Sun, 21 Jun 2020 18:11:36: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 18:11:36: #2 alternative fragment length(s) may be 45 bps INFO @ Sun, 21 Jun 2020 18:11:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.05_model.r WARNING @ Sun, 21 Jun 2020 18:11:36: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:11:36: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sun, 21 Jun 2020 18:11:36: #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 18:11:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:11:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:11:39: 2000000 INFO @ Sun, 21 Jun 2020 18:11:42: 6000000 INFO @ Sun, 21 Jun 2020 18:11:46: 3000000 INFO @ Sun, 21 Jun 2020 18:11:50: 7000000 INFO @ Sun, 21 Jun 2020 18:11:53: 4000000 INFO @ Sun, 21 Jun 2020 18:11:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:11:59: 8000000 INFO @ Sun, 21 Jun 2020 18:12:01: 5000000 INFO @ Sun, 21 Jun 2020 18:12:08: 9000000 INFO @ Sun, 21 Jun 2020 18:12:09: 6000000 INFO @ Sun, 21 Jun 2020 18:12:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:12:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:12:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.05_summits.bed INFO @ Sun, 21 Jun 2020 18:12:10: Done! pass1 - making usageList (845 chroms): 3 millis pass2 - checking and writing primary data (9242 records, 4 fields): 56 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:12:16: 7000000 INFO @ Sun, 21 Jun 2020 18:12:17: 10000000 INFO @ Sun, 21 Jun 2020 18:12:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:12:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:12:22: #1 total tags in treatment: 10590536 INFO @ Sun, 21 Jun 2020 18:12:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:12:22: #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 18:12:23: #1 tags after filtering in treatment: 10590533 INFO @ Sun, 21 Jun 2020 18:12:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:12:23: #1 finished! INFO @ Sun, 21 Jun 2020 18:12:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:12:23: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:12:24: #2 number of paired peaks: 2852 INFO @ Sun, 21 Jun 2020 18:12:24: start model_add_line... INFO @ Sun, 21 Jun 2020 18:12:24: start X-correlation... INFO @ Sun, 21 Jun 2020 18:12:24: end of X-cor INFO @ Sun, 21 Jun 2020 18:12:24: #2 finished! INFO @ Sun, 21 Jun 2020 18:12:24: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 18:12:24: #2 alternative fragment length(s) may be 45 bps INFO @ Sun, 21 Jun 2020 18:12:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.10_model.r WARNING @ Sun, 21 Jun 2020 18:12:24: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:12:24: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sun, 21 Jun 2020 18:12:24: #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 18:12:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:12:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:12:24: 8000000 INFO @ Sun, 21 Jun 2020 18:12:33: 9000000 INFO @ Sun, 21 Jun 2020 18:12:41: 10000000 INFO @ Sun, 21 Jun 2020 18:12:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:12:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:12:46: #1 total tags in treatment: 10590536 INFO @ Sun, 21 Jun 2020 18:12:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:12:46: #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 18:12:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:12:46: #1 tags after filtering in treatment: 10590533 INFO @ Sun, 21 Jun 2020 18:12:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:12:46: #1 finished! INFO @ Sun, 21 Jun 2020 18:12:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:12:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:12:47: #2 number of paired peaks: 2852 INFO @ Sun, 21 Jun 2020 18:12:47: start model_add_line... INFO @ Sun, 21 Jun 2020 18:12:48: start X-correlation... INFO @ Sun, 21 Jun 2020 18:12:48: end of X-cor INFO @ Sun, 21 Jun 2020 18:12:48: #2 finished! INFO @ Sun, 21 Jun 2020 18:12:48: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 18:12:48: #2 alternative fragment length(s) may be 45 bps INFO @ Sun, 21 Jun 2020 18:12:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.20_model.r WARNING @ Sun, 21 Jun 2020 18:12:48: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:12:48: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sun, 21 Jun 2020 18:12:48: #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 18:12:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:12:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:12:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:12:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:12:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.10_summits.bed INFO @ Sun, 21 Jun 2020 18:12:58: Done! pass1 - making usageList (645 chroms): 2 millis pass2 - checking and writing primary data (6053 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:13:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:13:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:13:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:13:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX152090/SRX152090.20_summits.bed INFO @ Sun, 21 Jun 2020 18:13:21: Done! pass1 - making usageList (207 chroms): 2 millis pass2 - checking and writing primary data (2704 records, 4 fields): 14 millis CompletedMACS2peakCalling