Job ID = 6452617 SRX = SRX018631 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:03:23 prefetch.2.10.7: 1) Downloading 'SRR039099'... 2020-06-21T08:03:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:04:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:04:20 prefetch.2.10.7: 'SRR039099' is valid 2020-06-21T08:04:20 prefetch.2.10.7: 1) 'SRR039099' was downloaded successfully Read 3122778 spots for SRR039099/SRR039099.sra Written 3122778 spots for SRR039099/SRR039099.sra 2020-06-21T08:04:39 prefetch.2.10.7: 1) Downloading 'SRR039100'... 2020-06-21T08:04:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:05:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:05:04 prefetch.2.10.7: 'SRR039100' is valid 2020-06-21T08:05:04 prefetch.2.10.7: 1) 'SRR039100' was downloaded successfully Read 3254949 spots for SRR039100/SRR039100.sra Written 3254949 spots for SRR039100/SRR039100.sra 2020-06-21T08:05:23 prefetch.2.10.7: 1) Downloading 'SRR039101'... 2020-06-21T08:05:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:06:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:06:01 prefetch.2.10.7: 'SRR039101' is valid 2020-06-21T08:06:01 prefetch.2.10.7: 1) 'SRR039101' was downloaded successfully Read 3345566 spots for SRR039101/SRR039101.sra Written 3345566 spots for SRR039101/SRR039101.sra 2020-06-21T08:06:21 prefetch.2.10.7: 1) Downloading 'SRR039102'... 2020-06-21T08:06:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:06:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:06:54 prefetch.2.10.7: 'SRR039102' is valid 2020-06-21T08:06:54 prefetch.2.10.7: 1) 'SRR039102' was downloaded successfully Read 3413820 spots for SRR039102/SRR039102.sra Written 3413820 spots for SRR039102/SRR039102.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: 00:02:23 13137113 reads; of these: 13137113 (100.00%) were unpaired; of these: 4178803 (31.81%) aligned 0 times 6219335 (47.34%) aligned exactly 1 time 2738975 (20.85%) aligned >1 times 68.19% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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_rmdupse_core] 1120946 / 8958310 = 0.1251 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 17:12:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.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 17:12:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:12:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:12:17: 1000000 INFO @ Sun, 21 Jun 2020 17:12:23: 2000000 INFO @ Sun, 21 Jun 2020 17:12:29: 3000000 INFO @ Sun, 21 Jun 2020 17:12:35: 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 17:12:40: 5000000 INFO @ Sun, 21 Jun 2020 17:12:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.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 17:12:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:12:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:12:46: 6000000 INFO @ Sun, 21 Jun 2020 17:12:47: 1000000 INFO @ Sun, 21 Jun 2020 17:12:53: 7000000 INFO @ Sun, 21 Jun 2020 17:12:53: 2000000 INFO @ Sun, 21 Jun 2020 17:12:58: #1 tag size is determined as 39 bps INFO @ Sun, 21 Jun 2020 17:12:58: #1 tag size = 39 INFO @ Sun, 21 Jun 2020 17:12:58: #1 total tags in treatment: 7837364 INFO @ Sun, 21 Jun 2020 17:12:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:12:58: #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 17:12:58: #1 tags after filtering in treatment: 7837252 INFO @ Sun, 21 Jun 2020 17:12:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:12:58: #1 finished! INFO @ Sun, 21 Jun 2020 17:12:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:12:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:12:58: 3000000 INFO @ Sun, 21 Jun 2020 17:12:59: #2 number of paired peaks: 1219 INFO @ Sun, 21 Jun 2020 17:12:59: start model_add_line... INFO @ Sun, 21 Jun 2020 17:12:59: start X-correlation... INFO @ Sun, 21 Jun 2020 17:12:59: end of X-cor INFO @ Sun, 21 Jun 2020 17:12:59: #2 finished! INFO @ Sun, 21 Jun 2020 17:12:59: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 17:12:59: #2 alternative fragment length(s) may be 4,69 bps INFO @ Sun, 21 Jun 2020 17:12:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.05_model.r WARNING @ Sun, 21 Jun 2020 17:12:59: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:12:59: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Sun, 21 Jun 2020 17:12:59: #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 17:12:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:12:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:13:04: 4000000 INFO @ Sun, 21 Jun 2020 17:13:09: 5000000 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 17:13:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.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 17:13:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:13:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:13:14: 6000000 INFO @ Sun, 21 Jun 2020 17:13:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:13:18: 1000000 INFO @ Sun, 21 Jun 2020 17:13:20: 7000000 INFO @ Sun, 21 Jun 2020 17:13:23: 2000000 INFO @ Sun, 21 Jun 2020 17:13:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:13:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:13:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.05_summits.bed INFO @ Sun, 21 Jun 2020 17:13:24: Done! pass1 - making usageList (582 chroms): 1 millis pass2 - checking and writing primary data (2579 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:13:25: #1 tag size is determined as 39 bps INFO @ Sun, 21 Jun 2020 17:13:25: #1 tag size = 39 INFO @ Sun, 21 Jun 2020 17:13:25: #1 total tags in treatment: 7837364 INFO @ Sun, 21 Jun 2020 17:13:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:13:25: #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 17:13:25: #1 tags after filtering in treatment: 7837252 INFO @ Sun, 21 Jun 2020 17:13:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:13:25: #1 finished! INFO @ Sun, 21 Jun 2020 17:13:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:13:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:13:26: #2 number of paired peaks: 1219 INFO @ Sun, 21 Jun 2020 17:13:26: start model_add_line... INFO @ Sun, 21 Jun 2020 17:13:26: start X-correlation... INFO @ Sun, 21 Jun 2020 17:13:26: end of X-cor INFO @ Sun, 21 Jun 2020 17:13:26: #2 finished! INFO @ Sun, 21 Jun 2020 17:13:26: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 17:13:26: #2 alternative fragment length(s) may be 4,69 bps INFO @ Sun, 21 Jun 2020 17:13:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.10_model.r WARNING @ Sun, 21 Jun 2020 17:13:26: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:13:26: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Sun, 21 Jun 2020 17:13:26: #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 17:13:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:13:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:13:29: 3000000 INFO @ Sun, 21 Jun 2020 17:13:34: 4000000 INFO @ Sun, 21 Jun 2020 17:13:39: 5000000 INFO @ Sun, 21 Jun 2020 17:13:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:13:45: 6000000 INFO @ Sun, 21 Jun 2020 17:13:50: 7000000 INFO @ Sun, 21 Jun 2020 17:13:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:13:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:13:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.10_summits.bed INFO @ Sun, 21 Jun 2020 17:13:51: Done! pass1 - making usageList (305 chroms): 1 millis pass2 - checking and writing primary data (1003 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:13:55: #1 tag size is determined as 39 bps INFO @ Sun, 21 Jun 2020 17:13:55: #1 tag size = 39 INFO @ Sun, 21 Jun 2020 17:13:55: #1 total tags in treatment: 7837364 INFO @ Sun, 21 Jun 2020 17:13:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:13:55: #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 17:13:55: #1 tags after filtering in treatment: 7837252 INFO @ Sun, 21 Jun 2020 17:13:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:13:55: #1 finished! INFO @ Sun, 21 Jun 2020 17:13:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:13:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:13:56: #2 number of paired peaks: 1219 INFO @ Sun, 21 Jun 2020 17:13:56: start model_add_line... INFO @ Sun, 21 Jun 2020 17:13:56: start X-correlation... INFO @ Sun, 21 Jun 2020 17:13:56: end of X-cor INFO @ Sun, 21 Jun 2020 17:13:56: #2 finished! INFO @ Sun, 21 Jun 2020 17:13:56: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 17:13:56: #2 alternative fragment length(s) may be 4,69 bps INFO @ Sun, 21 Jun 2020 17:13:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.20_model.r WARNING @ Sun, 21 Jun 2020 17:13:56: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:13:56: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Sun, 21 Jun 2020 17:13:56: #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 17:13:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:13:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:14:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:14:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:14:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:14:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX018631/SRX018631.20_summits.bed INFO @ Sun, 21 Jun 2020 17:14:22: Done! pass1 - making usageList (133 chroms): 1 millis pass2 - checking and writing primary data (405 records, 4 fields): 7 millis CompletedMACS2peakCalling