Job ID = 6454433 SRX = SRX2055961 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:04:19 prefetch.2.10.7: 1) Downloading 'SRR4069193'... 2020-06-21T09:04:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:07:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:07:55 prefetch.2.10.7: 1) 'SRR4069193' was downloaded successfully Read 23814936 spots for SRR4069193/SRR4069193.sra Written 23814936 spots for SRR4069193/SRR4069193.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: 00:06:51 23814936 reads; of these: 23814936 (100.00%) were unpaired; of these: 6947794 (29.17%) aligned 0 times 10798719 (45.34%) aligned exactly 1 time 6068423 (25.48%) aligned >1 times 70.83% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 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] 6306730 / 16867142 = 0.3739 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 18:19:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.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 18:19:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:35: 1000000 INFO @ Sun, 21 Jun 2020 18:19:39: 2000000 INFO @ Sun, 21 Jun 2020 18:19:44: 3000000 INFO @ Sun, 21 Jun 2020 18:19:49: 4000000 INFO @ Sun, 21 Jun 2020 18:19:54: 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 18:19:59: 6000000 INFO @ Sun, 21 Jun 2020 18:19:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.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 18:19:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:20:04: 7000000 INFO @ Sun, 21 Jun 2020 18:20:05: 1000000 INFO @ Sun, 21 Jun 2020 18:20:09: 8000000 INFO @ Sun, 21 Jun 2020 18:20:10: 2000000 INFO @ Sun, 21 Jun 2020 18:20:14: 9000000 INFO @ Sun, 21 Jun 2020 18:20:16: 3000000 INFO @ Sun, 21 Jun 2020 18:20:19: 10000000 INFO @ Sun, 21 Jun 2020 18:20:21: 4000000 INFO @ Sun, 21 Jun 2020 18:20:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:20:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:20:22: #1 total tags in treatment: 10560412 INFO @ Sun, 21 Jun 2020 18:20:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:22: #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 18:20:23: #1 tags after filtering in treatment: 10560328 INFO @ Sun, 21 Jun 2020 18:20:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:23: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:24: #2 number of paired peaks: 2462 INFO @ Sun, 21 Jun 2020 18:20:24: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:24: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:24: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:24: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:24: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 18:20:24: #2 alternative fragment length(s) may be 2,60 bps INFO @ Sun, 21 Jun 2020 18:20:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.05_model.r WARNING @ Sun, 21 Jun 2020 18:20:24: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:20:24: #2 You may need to consider one of the other alternative d(s): 2,60 WARNING @ Sun, 21 Jun 2020 18:20:24: #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 18:20:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:27: 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 @ Sun, 21 Jun 2020 18:20:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.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 18:20:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:20:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:20:32: 6000000 INFO @ Sun, 21 Jun 2020 18:20:34: 1000000 INFO @ Sun, 21 Jun 2020 18:20:38: 7000000 INFO @ Sun, 21 Jun 2020 18:20:40: 2000000 INFO @ Sun, 21 Jun 2020 18:20:43: 8000000 INFO @ Sun, 21 Jun 2020 18:20:45: 3000000 INFO @ Sun, 21 Jun 2020 18:20:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:20:49: 9000000 INFO @ Sun, 21 Jun 2020 18:20:50: 4000000 INFO @ Sun, 21 Jun 2020 18:20:55: 10000000 INFO @ Sun, 21 Jun 2020 18:20:55: 5000000 INFO @ Sun, 21 Jun 2020 18:20:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:20:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:20:58: #1 total tags in treatment: 10560412 INFO @ Sun, 21 Jun 2020 18:20:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:58: #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 18:20:59: #1 tags after filtering in treatment: 10560328 INFO @ Sun, 21 Jun 2020 18:20:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:59: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:20:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:20:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.05_summits.bed INFO @ Sun, 21 Jun 2020 18:21:00: Done! INFO @ Sun, 21 Jun 2020 18:21:00: #2 number of paired peaks: 2462 INFO @ Sun, 21 Jun 2020 18:21:00: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:00: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:00: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:00: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:00: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 18:21:00: #2 alternative fragment length(s) may be 2,60 bps INFO @ Sun, 21 Jun 2020 18:21:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.10_model.r WARNING @ Sun, 21 Jun 2020 18:21:00: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:21:00: #2 You may need to consider one of the other alternative d(s): 2,60 WARNING @ Sun, 21 Jun 2020 18:21:00: #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 18:21:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:21:00: 6000000 pass1 - making usageList (677 chroms): 3 millis pass2 - checking and writing primary data (3669 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:21:05: 7000000 INFO @ Sun, 21 Jun 2020 18:21:10: 8000000 INFO @ Sun, 21 Jun 2020 18:21:16: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:21:21: 10000000 INFO @ Sun, 21 Jun 2020 18:21:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:21:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:21:24: #1 total tags in treatment: 10560412 INFO @ Sun, 21 Jun 2020 18:21:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:21:24: #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 18:21:24: #1 tags after filtering in treatment: 10560328 INFO @ Sun, 21 Jun 2020 18:21:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:21:24: #1 finished! INFO @ Sun, 21 Jun 2020 18:21:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:21:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:21:25: #2 number of paired peaks: 2462 INFO @ Sun, 21 Jun 2020 18:21:25: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:26: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:26: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:26: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:26: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 18:21:26: #2 alternative fragment length(s) may be 2,60 bps INFO @ Sun, 21 Jun 2020 18:21:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.20_model.r WARNING @ Sun, 21 Jun 2020 18:21:26: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:21:26: #2 You may need to consider one of the other alternative d(s): 2,60 WARNING @ Sun, 21 Jun 2020 18:21:26: #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 18:21:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:21:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.10_summits.bed INFO @ Sun, 21 Jun 2020 18:21:35: Done! pass1 - making usageList (548 chroms): 2 millis pass2 - checking and writing primary data (2262 records, 4 fields): 22 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:21:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:22:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:22:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:22:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055961/SRX2055961.20_summits.bed INFO @ Sun, 21 Jun 2020 18:22:03: Done! pass1 - making usageList (397 chroms): 1 millis pass2 - checking and writing primary data (1039 records, 4 fields): 14 millis CompletedMACS2peakCalling