Job ID = 6498300 SRX = SRX467111 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:34:30 prefetch.2.10.7: 1) Downloading 'SRR1164535'... 2020-06-25T23:34:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:35:48 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:35:48 prefetch.2.10.7: 'SRR1164535' is valid 2020-06-25T23:35:48 prefetch.2.10.7: 1) 'SRR1164535' was downloaded successfully Read 12991045 spots for SRR1164535/SRR1164535.sra Written 12991045 spots for SRR1164535/SRR1164535.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: 00:04:54 12991045 reads; of these: 12991045 (100.00%) were unpaired; of these: 807666 (6.22%) aligned 0 times 7536987 (58.02%) aligned exactly 1 time 4646392 (35.77%) aligned >1 times 93.78% overall alignment rate Time searching: 00:04:54 Overall time: 00:04:54 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 8 files... [bam_rmdupse_core] 1544179 / 12183379 = 0.1267 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 @ Fri, 26 Jun 2020 08:44:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.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 @ Fri, 26 Jun 2020 08:44:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:44:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:45:00: 1000000 INFO @ Fri, 26 Jun 2020 08:45:06: 2000000 INFO @ Fri, 26 Jun 2020 08:45:12: 3000000 INFO @ Fri, 26 Jun 2020 08:45:19: 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 @ Fri, 26 Jun 2020 08:45:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.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 @ Fri, 26 Jun 2020 08:45:23: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:45:23: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:45:25: 5000000 INFO @ Fri, 26 Jun 2020 08:45:30: 1000000 INFO @ Fri, 26 Jun 2020 08:45:32: 6000000 INFO @ Fri, 26 Jun 2020 08:45:37: 2000000 INFO @ Fri, 26 Jun 2020 08:45:39: 7000000 INFO @ Fri, 26 Jun 2020 08:45:44: 3000000 INFO @ Fri, 26 Jun 2020 08:45:46: 8000000 INFO @ Fri, 26 Jun 2020 08:45:51: 4000000 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 @ Fri, 26 Jun 2020 08:45:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.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 @ Fri, 26 Jun 2020 08:45:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:45:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:45:53: 9000000 INFO @ Fri, 26 Jun 2020 08:45:58: 5000000 INFO @ Fri, 26 Jun 2020 08:46:01: 1000000 INFO @ Fri, 26 Jun 2020 08:46:01: 10000000 INFO @ Fri, 26 Jun 2020 08:46:05: 6000000 INFO @ Fri, 26 Jun 2020 08:46:05: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:46:05: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:46:05: #1 total tags in treatment: 10639200 INFO @ Fri, 26 Jun 2020 08:46:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:46:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:46:05: #1 tags after filtering in treatment: 10639200 INFO @ Fri, 26 Jun 2020 08:46:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:46:05: #1 finished! INFO @ Fri, 26 Jun 2020 08:46:05: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:46:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:46:06: #2 number of paired peaks: 1253 INFO @ Fri, 26 Jun 2020 08:46:06: start model_add_line... INFO @ Fri, 26 Jun 2020 08:46:06: start X-correlation... INFO @ Fri, 26 Jun 2020 08:46:06: end of X-cor INFO @ Fri, 26 Jun 2020 08:46:06: #2 finished! INFO @ Fri, 26 Jun 2020 08:46:06: #2 predicted fragment length is 54 bps INFO @ Fri, 26 Jun 2020 08:46:06: #2 alternative fragment length(s) may be 4,54,546 bps INFO @ Fri, 26 Jun 2020 08:46:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.05_model.r WARNING @ Fri, 26 Jun 2020 08:46:06: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:46:06: #2 You may need to consider one of the other alternative d(s): 4,54,546 WARNING @ Fri, 26 Jun 2020 08:46:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:46:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:46:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:46:08: 2000000 INFO @ Fri, 26 Jun 2020 08:46:12: 7000000 INFO @ Fri, 26 Jun 2020 08:46:15: 3000000 INFO @ Fri, 26 Jun 2020 08:46:19: 8000000 INFO @ Fri, 26 Jun 2020 08:46:22: 4000000 INFO @ Fri, 26 Jun 2020 08:46:26: 9000000 INFO @ Fri, 26 Jun 2020 08:46:29: 5000000 INFO @ Fri, 26 Jun 2020 08:46:29: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:46:33: 10000000 INFO @ Fri, 26 Jun 2020 08:46:35: 6000000 INFO @ Fri, 26 Jun 2020 08:46:37: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:46:37: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:46:37: #1 total tags in treatment: 10639200 INFO @ Fri, 26 Jun 2020 08:46:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:46:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:46:37: #1 tags after filtering in treatment: 10639200 INFO @ Fri, 26 Jun 2020 08:46:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:46:37: #1 finished! INFO @ Fri, 26 Jun 2020 08:46:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:46:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:46:38: #2 number of paired peaks: 1253 INFO @ Fri, 26 Jun 2020 08:46:38: start model_add_line... INFO @ Fri, 26 Jun 2020 08:46:38: start X-correlation... INFO @ Fri, 26 Jun 2020 08:46:38: end of X-cor INFO @ Fri, 26 Jun 2020 08:46:38: #2 finished! INFO @ Fri, 26 Jun 2020 08:46:38: #2 predicted fragment length is 54 bps INFO @ Fri, 26 Jun 2020 08:46:38: #2 alternative fragment length(s) may be 4,54,546 bps INFO @ Fri, 26 Jun 2020 08:46:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.10_model.r WARNING @ Fri, 26 Jun 2020 08:46:38: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:46:38: #2 You may need to consider one of the other alternative d(s): 4,54,546 WARNING @ Fri, 26 Jun 2020 08:46:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:46:38: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:46:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:46:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:46:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:46:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.05_summits.bed INFO @ Fri, 26 Jun 2020 08:46:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3404 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:46:42: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:46:48: 8000000 INFO @ Fri, 26 Jun 2020 08:46:54: 9000000 INFO @ Fri, 26 Jun 2020 08:47:01: 10000000 INFO @ Fri, 26 Jun 2020 08:47:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:47:05: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:47:05: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:47:05: #1 total tags in treatment: 10639200 INFO @ Fri, 26 Jun 2020 08:47:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:47:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:47:05: #1 tags after filtering in treatment: 10639200 INFO @ Fri, 26 Jun 2020 08:47:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:47:05: #1 finished! INFO @ Fri, 26 Jun 2020 08:47:05: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:47:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:47:06: #2 number of paired peaks: 1253 INFO @ Fri, 26 Jun 2020 08:47:06: start model_add_line... INFO @ Fri, 26 Jun 2020 08:47:06: start X-correlation... INFO @ Fri, 26 Jun 2020 08:47:06: end of X-cor INFO @ Fri, 26 Jun 2020 08:47:06: #2 finished! INFO @ Fri, 26 Jun 2020 08:47:06: #2 predicted fragment length is 54 bps INFO @ Fri, 26 Jun 2020 08:47:06: #2 alternative fragment length(s) may be 4,54,546 bps INFO @ Fri, 26 Jun 2020 08:47:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.20_model.r WARNING @ Fri, 26 Jun 2020 08:47:06: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:47:06: #2 You may need to consider one of the other alternative d(s): 4,54,546 WARNING @ Fri, 26 Jun 2020 08:47:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:47:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:47:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:47:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:47:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:47:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.10_summits.bed INFO @ Fri, 26 Jun 2020 08:47:12: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2256 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:47:29: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:47:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:47:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:47:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467111/SRX467111.20_summits.bed INFO @ Fri, 26 Jun 2020 08:47:40: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (986 records, 4 fields): 2 millis CompletedMACS2peakCalling