Job ID = 6454311 SRX = SRX197582 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:58:34 prefetch.2.10.7: 1) Downloading 'SRR597010'... 2020-06-21T08:58:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:02:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:02:26 prefetch.2.10.7: 'SRR597010' is valid 2020-06-21T09:02:26 prefetch.2.10.7: 1) 'SRR597010' was downloaded successfully Read 23769758 spots for SRR597010/SRR597010.sra Written 23769758 spots for SRR597010/SRR597010.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: 00:03:55 23769758 reads; of these: 23769758 (100.00%) were unpaired; of these: 11931107 (50.19%) aligned 0 times 8275252 (34.81%) aligned exactly 1 time 3563399 (14.99%) aligned >1 times 49.81% overall alignment rate Time searching: 00:03:55 Overall time: 00:03:55 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] 2718737 / 11838651 = 0.2296 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 18:10:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.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 18:10:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:10:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:10:18: 1000000 INFO @ Sun, 21 Jun 2020 18:10:23: 2000000 INFO @ Sun, 21 Jun 2020 18:10:28: 3000000 INFO @ Sun, 21 Jun 2020 18:10:33: 4000000 INFO @ Sun, 21 Jun 2020 18:10:37: 5000000 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 18:10:42: 6000000 INFO @ Sun, 21 Jun 2020 18:10:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.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 18:10:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:10:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:10:48: 7000000 INFO @ Sun, 21 Jun 2020 18:10:48: 1000000 INFO @ Sun, 21 Jun 2020 18:10:53: 8000000 INFO @ Sun, 21 Jun 2020 18:10:54: 2000000 INFO @ Sun, 21 Jun 2020 18:10:59: 9000000 INFO @ Sun, 21 Jun 2020 18:10:59: 3000000 INFO @ Sun, 21 Jun 2020 18:11:00: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:11:00: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:11:00: #1 total tags in treatment: 9119914 INFO @ Sun, 21 Jun 2020 18:11:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:11:00: #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 18:11:00: #1 tags after filtering in treatment: 9119913 INFO @ Sun, 21 Jun 2020 18:11:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:11:00: #1 finished! INFO @ Sun, 21 Jun 2020 18:11:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:11:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:11:01: #2 number of paired peaks: 1172 INFO @ Sun, 21 Jun 2020 18:11:01: start model_add_line... INFO @ Sun, 21 Jun 2020 18:11:01: start X-correlation... INFO @ Sun, 21 Jun 2020 18:11:01: end of X-cor INFO @ Sun, 21 Jun 2020 18:11:01: #2 finished! INFO @ Sun, 21 Jun 2020 18:11:01: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 18:11:01: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 18:11:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.05_model.r WARNING @ Sun, 21 Jun 2020 18:11:01: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:11:01: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 18:11:01: #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 18:11:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:11:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:11:04: 4000000 INFO @ Sun, 21 Jun 2020 18:11:09: 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 18:11:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.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 18:11:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:11:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:11:14: 6000000 INFO @ Sun, 21 Jun 2020 18:11:18: 1000000 INFO @ Sun, 21 Jun 2020 18:11:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:11:19: 7000000 INFO @ Sun, 21 Jun 2020 18:11:24: 2000000 INFO @ Sun, 21 Jun 2020 18:11:25: 8000000 INFO @ Sun, 21 Jun 2020 18:11:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:11:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:11:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.05_summits.bed INFO @ Sun, 21 Jun 2020 18:11:28: Done! pass1 - making usageList (633 chroms): 2 millis pass2 - checking and writing primary data (2992 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:11:29: 3000000 INFO @ Sun, 21 Jun 2020 18:11:31: 9000000 INFO @ Sun, 21 Jun 2020 18:11:31: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:11:31: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:11:31: #1 total tags in treatment: 9119914 INFO @ Sun, 21 Jun 2020 18:11:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:11:31: #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 18:11:32: #1 tags after filtering in treatment: 9119913 INFO @ Sun, 21 Jun 2020 18:11:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:11:32: #1 finished! INFO @ Sun, 21 Jun 2020 18:11:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:11:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:11:33: #2 number of paired peaks: 1172 INFO @ Sun, 21 Jun 2020 18:11:33: start model_add_line... INFO @ Sun, 21 Jun 2020 18:11:33: start X-correlation... INFO @ Sun, 21 Jun 2020 18:11:33: end of X-cor INFO @ Sun, 21 Jun 2020 18:11:33: #2 finished! INFO @ Sun, 21 Jun 2020 18:11:33: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 18:11:33: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 18:11:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.10_model.r WARNING @ Sun, 21 Jun 2020 18:11:33: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:11:33: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 18:11:33: #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 18:11:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:11:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:11:34: 4000000 INFO @ Sun, 21 Jun 2020 18:11:39: 5000000 INFO @ Sun, 21 Jun 2020 18:11:44: 6000000 INFO @ Sun, 21 Jun 2020 18:11:49: 7000000 INFO @ Sun, 21 Jun 2020 18:11:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:11:54: 8000000 INFO @ Sun, 21 Jun 2020 18:11:59: 9000000 INFO @ Sun, 21 Jun 2020 18:12:00: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:12:00: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:12:00: #1 total tags in treatment: 9119914 INFO @ Sun, 21 Jun 2020 18:12:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:12:00: #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 18:12:01: #1 tags after filtering in treatment: 9119913 INFO @ Sun, 21 Jun 2020 18:12:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:12:01: #1 finished! INFO @ Sun, 21 Jun 2020 18:12:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:12:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:12:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:12:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:12:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.10_summits.bed INFO @ Sun, 21 Jun 2020 18:12:01: Done! pass1 - making usageList (493 chroms): 1 millis pass2 - checking and writing primary data (1934 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:12:01: #2 number of paired peaks: 1172 INFO @ Sun, 21 Jun 2020 18:12:01: start model_add_line... INFO @ Sun, 21 Jun 2020 18:12:01: start X-correlation... INFO @ Sun, 21 Jun 2020 18:12:01: end of X-cor INFO @ Sun, 21 Jun 2020 18:12:01: #2 finished! INFO @ Sun, 21 Jun 2020 18:12:01: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 18:12:01: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 18:12:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.20_model.r WARNING @ Sun, 21 Jun 2020 18:12:01: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:12:01: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 18:12:01: #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 18:12:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:12:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:12:19: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:12:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:12:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:12:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197582/SRX197582.20_summits.bed INFO @ Sun, 21 Jun 2020 18:12:29: Done! pass1 - making usageList (199 chroms): 0 millis pass2 - checking and writing primary data (459 records, 4 fields): 7 millis CompletedMACS2peakCalling