Job ID = 6527479 SRX = SRX025480 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:52:09 prefetch.2.10.7: 1) Downloading 'SRR063881'... 2020-06-29T12:52:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:52:35 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:52:35 prefetch.2.10.7: 'SRR063881' is valid 2020-06-29T12:52:35 prefetch.2.10.7: 1) 'SRR063881' was downloaded successfully Read 4099721 spots for SRR063881/SRR063881.sra Written 4099721 spots for SRR063881/SRR063881.sra 2020-06-29T12:52:56 prefetch.2.10.7: 1) Downloading 'SRR063882'... 2020-06-29T12:52:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:54:45 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:54:46 prefetch.2.10.7: 'SRR063882' is valid 2020-06-29T12:54:46 prefetch.2.10.7: 1) 'SRR063882' was downloaded successfully Read 26960866 spots for SRR063882/SRR063882.sra Written 26960866 spots for SRR063882/SRR063882.sra 2020-06-29T12:56:11 prefetch.2.10.7: 1) Downloading 'SRR063883'... 2020-06-29T12:56:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:58:02 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:58:02 prefetch.2.10.7: 'SRR063883' is valid 2020-06-29T12:58:02 prefetch.2.10.7: 1) 'SRR063883' was downloaded successfully Read 24588013 spots for SRR063883/SRR063883.sra Written 24588013 spots for SRR063883/SRR063883.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: 00:15:43 55648600 reads; of these: 55648600 (100.00%) were unpaired; of these: 1774435 (3.19%) aligned 0 times 39462477 (70.91%) aligned exactly 1 time 14411688 (25.90%) aligned >1 times 96.81% overall alignment rate Time searching: 00:15:43 Overall time: 00:15:43 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 33167020 / 53874165 = 0.6156 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 @ Mon, 29 Jun 2020 22:31:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.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 @ Mon, 29 Jun 2020 22:31:29: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:31:29: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:31:34: 1000000 INFO @ Mon, 29 Jun 2020 22:31:40: 2000000 INFO @ Mon, 29 Jun 2020 22:31:45: 3000000 INFO @ Mon, 29 Jun 2020 22:31:51: 4000000 INFO @ Mon, 29 Jun 2020 22:31:57: 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 @ Mon, 29 Jun 2020 22:31:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.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 @ Mon, 29 Jun 2020 22:31:59: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:31:59: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:32:02: 6000000 INFO @ Mon, 29 Jun 2020 22:32:04: 1000000 INFO @ Mon, 29 Jun 2020 22:32:08: 7000000 INFO @ Mon, 29 Jun 2020 22:32:10: 2000000 INFO @ Mon, 29 Jun 2020 22:32:14: 8000000 INFO @ Mon, 29 Jun 2020 22:32:15: 3000000 INFO @ Mon, 29 Jun 2020 22:32:20: 9000000 INFO @ Mon, 29 Jun 2020 22:32:21: 4000000 INFO @ Mon, 29 Jun 2020 22:32:25: 10000000 INFO @ Mon, 29 Jun 2020 22:32:27: 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 @ Mon, 29 Jun 2020 22:32:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.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 @ Mon, 29 Jun 2020 22:32:29: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:32:29: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:32:31: 11000000 INFO @ Mon, 29 Jun 2020 22:32:32: 6000000 INFO @ Mon, 29 Jun 2020 22:32:34: 1000000 INFO @ Mon, 29 Jun 2020 22:32:37: 12000000 INFO @ Mon, 29 Jun 2020 22:32:38: 7000000 INFO @ Mon, 29 Jun 2020 22:32:39: 2000000 INFO @ Mon, 29 Jun 2020 22:32:43: 13000000 INFO @ Mon, 29 Jun 2020 22:32:44: 8000000 INFO @ Mon, 29 Jun 2020 22:32:44: 3000000 INFO @ Mon, 29 Jun 2020 22:32:49: 14000000 INFO @ Mon, 29 Jun 2020 22:32:49: 4000000 INFO @ Mon, 29 Jun 2020 22:32:50: 9000000 INFO @ Mon, 29 Jun 2020 22:32:54: 5000000 INFO @ Mon, 29 Jun 2020 22:32:55: 15000000 INFO @ Mon, 29 Jun 2020 22:32:56: 10000000 INFO @ Mon, 29 Jun 2020 22:32:59: 6000000 INFO @ Mon, 29 Jun 2020 22:33:01: 16000000 INFO @ Mon, 29 Jun 2020 22:33:02: 11000000 INFO @ Mon, 29 Jun 2020 22:33:04: 7000000 INFO @ Mon, 29 Jun 2020 22:33:07: 17000000 INFO @ Mon, 29 Jun 2020 22:33:08: 12000000 INFO @ Mon, 29 Jun 2020 22:33:09: 8000000 INFO @ Mon, 29 Jun 2020 22:33:13: 18000000 INFO @ Mon, 29 Jun 2020 22:33:14: 13000000 INFO @ Mon, 29 Jun 2020 22:33:14: 9000000 INFO @ Mon, 29 Jun 2020 22:33:19: 19000000 INFO @ Mon, 29 Jun 2020 22:33:19: 10000000 INFO @ Mon, 29 Jun 2020 22:33:20: 14000000 INFO @ Mon, 29 Jun 2020 22:33:24: 11000000 INFO @ Mon, 29 Jun 2020 22:33:25: 20000000 INFO @ Mon, 29 Jun 2020 22:33:26: 15000000 INFO @ Mon, 29 Jun 2020 22:33:29: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:33:29: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:33:29: #1 total tags in treatment: 20707145 INFO @ Mon, 29 Jun 2020 22:33:29: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:33:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:33:29: #1 tags after filtering in treatment: 20707145 INFO @ Mon, 29 Jun 2020 22:33:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:33:29: #1 finished! INFO @ Mon, 29 Jun 2020 22:33:29: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:33:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:33:30: 12000000 INFO @ Mon, 29 Jun 2020 22:33:31: #2 number of paired peaks: 301 WARNING @ Mon, 29 Jun 2020 22:33:31: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Mon, 29 Jun 2020 22:33:31: start model_add_line... INFO @ Mon, 29 Jun 2020 22:33:31: start X-correlation... INFO @ Mon, 29 Jun 2020 22:33:31: end of X-cor INFO @ Mon, 29 Jun 2020 22:33:31: #2 finished! INFO @ Mon, 29 Jun 2020 22:33:31: #2 predicted fragment length is 36 bps INFO @ Mon, 29 Jun 2020 22:33:31: #2 alternative fragment length(s) may be 36 bps INFO @ Mon, 29 Jun 2020 22:33:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.05_model.r WARNING @ Mon, 29 Jun 2020 22:33:31: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:33:31: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Mon, 29 Jun 2020 22:33:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:33:31: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:33:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:33:31: 16000000 INFO @ Mon, 29 Jun 2020 22:33:35: 13000000 INFO @ Mon, 29 Jun 2020 22:33:37: 17000000 INFO @ Mon, 29 Jun 2020 22:33:40: 14000000 INFO @ Mon, 29 Jun 2020 22:33:43: 18000000 INFO @ Mon, 29 Jun 2020 22:33:45: 15000000 INFO @ Mon, 29 Jun 2020 22:33:49: 19000000 INFO @ Mon, 29 Jun 2020 22:33:50: 16000000 INFO @ Mon, 29 Jun 2020 22:33:54: 20000000 INFO @ Mon, 29 Jun 2020 22:33:55: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:33:59: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:33:59: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:33:59: #1 total tags in treatment: 20707145 INFO @ Mon, 29 Jun 2020 22:33:59: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:33:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:33:59: #1 tags after filtering in treatment: 20707145 INFO @ Mon, 29 Jun 2020 22:33:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:33:59: #1 finished! INFO @ Mon, 29 Jun 2020 22:33:59: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:33:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:34:00: #2 number of paired peaks: 301 WARNING @ Mon, 29 Jun 2020 22:34:00: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Mon, 29 Jun 2020 22:34:00: start model_add_line... INFO @ Mon, 29 Jun 2020 22:34:00: start X-correlation... INFO @ Mon, 29 Jun 2020 22:34:00: end of X-cor INFO @ Mon, 29 Jun 2020 22:34:00: #2 finished! INFO @ Mon, 29 Jun 2020 22:34:00: #2 predicted fragment length is 36 bps INFO @ Mon, 29 Jun 2020 22:34:00: #2 alternative fragment length(s) may be 36 bps INFO @ Mon, 29 Jun 2020 22:34:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.10_model.r WARNING @ Mon, 29 Jun 2020 22:34:00: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:34:00: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Mon, 29 Jun 2020 22:34:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:34:00: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:34:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:34:00: 18000000 INFO @ Mon, 29 Jun 2020 22:34:06: 19000000 INFO @ Mon, 29 Jun 2020 22:34:11: 20000000 INFO @ Mon, 29 Jun 2020 22:34:12: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:34:14: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:34:14: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:34:14: #1 total tags in treatment: 20707145 INFO @ Mon, 29 Jun 2020 22:34:14: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:34:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:34:15: #1 tags after filtering in treatment: 20707145 INFO @ Mon, 29 Jun 2020 22:34:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:34:15: #1 finished! INFO @ Mon, 29 Jun 2020 22:34:15: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:34:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:34:16: #2 number of paired peaks: 301 WARNING @ Mon, 29 Jun 2020 22:34:16: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Mon, 29 Jun 2020 22:34:16: start model_add_line... INFO @ Mon, 29 Jun 2020 22:34:16: start X-correlation... INFO @ Mon, 29 Jun 2020 22:34:16: end of X-cor INFO @ Mon, 29 Jun 2020 22:34:16: #2 finished! INFO @ Mon, 29 Jun 2020 22:34:16: #2 predicted fragment length is 36 bps INFO @ Mon, 29 Jun 2020 22:34:16: #2 alternative fragment length(s) may be 36 bps INFO @ Mon, 29 Jun 2020 22:34:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.20_model.r WARNING @ Mon, 29 Jun 2020 22:34:16: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:34:16: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Mon, 29 Jun 2020 22:34:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:34:16: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:34:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:34:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:34:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:34:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.05_summits.bed INFO @ Mon, 29 Jun 2020 22:34:33: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2765 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:34:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:34:59: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:35:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:35:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:35:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.10_summits.bed INFO @ Mon, 29 Jun 2020 22:35:04: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1814 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:35:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:35:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:35:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX025480/SRX025480.20_summits.bed INFO @ Mon, 29 Jun 2020 22:35:19: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1152 records, 4 fields): 3 millis CompletedMACS2peakCalling