Job ID = 6367260 SRX = SRX323681 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:27:36 prefetch.2.10.7: 1) Downloading 'SRR935755'... 2020-06-15T23:27:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:29:34 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:29:35 prefetch.2.10.7: 'SRR935755' is valid 2020-06-15T23:29:35 prefetch.2.10.7: 1) 'SRR935755' was downloaded successfully Read 14347144 spots for SRR935755/SRR935755.sra Written 14347144 spots for SRR935755/SRR935755.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: 00:02:16 14347144 reads; of these: 14347144 (100.00%) were unpaired; of these: 1201620 (8.38%) aligned 0 times 9881157 (68.87%) aligned exactly 1 time 3264367 (22.75%) aligned >1 times 91.62% overall alignment rate Time searching: 00:02:16 Overall time: 00:02:16 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1956907 / 13145524 = 0.1489 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 @ Tue, 16 Jun 2020 08:35:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:35:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:02: 1000000 INFO @ Tue, 16 Jun 2020 08:36:08: 2000000 INFO @ Tue, 16 Jun 2020 08:36:14: 3000000 INFO @ Tue, 16 Jun 2020 08:36:19: 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 @ Tue, 16 Jun 2020 08:36:25: 5000000 INFO @ Tue, 16 Jun 2020 08:36:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:36:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:31: 6000000 INFO @ Tue, 16 Jun 2020 08:36:32: 1000000 INFO @ Tue, 16 Jun 2020 08:36:37: 7000000 INFO @ Tue, 16 Jun 2020 08:36:38: 2000000 INFO @ Tue, 16 Jun 2020 08:36:43: 8000000 INFO @ Tue, 16 Jun 2020 08:36:44: 3000000 INFO @ Tue, 16 Jun 2020 08:36:49: 9000000 INFO @ Tue, 16 Jun 2020 08:36:50: 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 @ Tue, 16 Jun 2020 08:36:55: 5000000 INFO @ Tue, 16 Jun 2020 08:36:55: 10000000 INFO @ Tue, 16 Jun 2020 08:36:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:36:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:37:01: 6000000 INFO @ Tue, 16 Jun 2020 08:37:02: 11000000 INFO @ Tue, 16 Jun 2020 08:37:02: 1000000 INFO @ Tue, 16 Jun 2020 08:37:03: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:37:03: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:37:03: #1 total tags in treatment: 11188617 INFO @ Tue, 16 Jun 2020 08:37:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:37:03: #1 tags after filtering in treatment: 11188617 INFO @ Tue, 16 Jun 2020 08:37:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:04: #2 number of paired peaks: 520 WARNING @ Tue, 16 Jun 2020 08:37:04: Fewer paired peaks (520) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 520 pairs to build model! INFO @ Tue, 16 Jun 2020 08:37:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:04: #2 predicted fragment length is 29 bps INFO @ Tue, 16 Jun 2020 08:37:04: #2 alternative fragment length(s) may be 1,29,585 bps INFO @ Tue, 16 Jun 2020 08:37:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.05_model.r WARNING @ Tue, 16 Jun 2020 08:37:04: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:37:04: #2 You may need to consider one of the other alternative d(s): 1,29,585 WARNING @ Tue, 16 Jun 2020 08:37:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:37:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:07: 7000000 INFO @ Tue, 16 Jun 2020 08:37:09: 2000000 INFO @ Tue, 16 Jun 2020 08:37:12: 8000000 INFO @ Tue, 16 Jun 2020 08:37:15: 3000000 INFO @ Tue, 16 Jun 2020 08:37:18: 9000000 INFO @ Tue, 16 Jun 2020 08:37:21: 4000000 INFO @ Tue, 16 Jun 2020 08:37:24: 10000000 INFO @ Tue, 16 Jun 2020 08:37:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:27: 5000000 INFO @ Tue, 16 Jun 2020 08:37:29: 11000000 INFO @ Tue, 16 Jun 2020 08:37:30: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:37:30: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:37:30: #1 total tags in treatment: 11188617 INFO @ Tue, 16 Jun 2020 08:37:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:37:30: #1 tags after filtering in treatment: 11188617 INFO @ Tue, 16 Jun 2020 08:37:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:31: #2 number of paired peaks: 520 WARNING @ Tue, 16 Jun 2020 08:37:31: Fewer paired peaks (520) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 520 pairs to build model! INFO @ Tue, 16 Jun 2020 08:37:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:31: #2 predicted fragment length is 29 bps INFO @ Tue, 16 Jun 2020 08:37:31: #2 alternative fragment length(s) may be 1,29,585 bps INFO @ Tue, 16 Jun 2020 08:37:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.10_model.r WARNING @ Tue, 16 Jun 2020 08:37:31: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:37:31: #2 You may need to consider one of the other alternative d(s): 1,29,585 WARNING @ Tue, 16 Jun 2020 08:37:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:37:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:33: 6000000 INFO @ Tue, 16 Jun 2020 08:37:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.05_summits.bed INFO @ Tue, 16 Jun 2020 08:37:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1297 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:37:39: 7000000 INFO @ Tue, 16 Jun 2020 08:37:45: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:37:50: 9000000 INFO @ Tue, 16 Jun 2020 08:37:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:56: 10000000 INFO @ Tue, 16 Jun 2020 08:38:01: 11000000 INFO @ Tue, 16 Jun 2020 08:38:03: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:38:03: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:38:03: #1 total tags in treatment: 11188617 INFO @ Tue, 16 Jun 2020 08:38:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:38:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:38:03: #1 tags after filtering in treatment: 11188617 INFO @ Tue, 16 Jun 2020 08:38:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:38:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:38:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:38:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:38:03: #2 number of paired peaks: 520 WARNING @ Tue, 16 Jun 2020 08:38:03: Fewer paired peaks (520) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 520 pairs to build model! INFO @ Tue, 16 Jun 2020 08:38:03: start model_add_line... INFO @ Tue, 16 Jun 2020 08:38:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:38:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:38:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:38:04: #2 predicted fragment length is 29 bps INFO @ Tue, 16 Jun 2020 08:38:04: #2 alternative fragment length(s) may be 1,29,585 bps INFO @ Tue, 16 Jun 2020 08:38:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.20_model.r WARNING @ Tue, 16 Jun 2020 08:38:04: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:38:04: #2 You may need to consider one of the other alternative d(s): 1,29,585 WARNING @ Tue, 16 Jun 2020 08:38:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:38:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:38:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:38:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:38:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:38:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.10_summits.bed INFO @ Tue, 16 Jun 2020 08:38:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (460 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:38:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:38:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:38:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:38:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX323681/SRX323681.20_summits.bed INFO @ Tue, 16 Jun 2020 08:38:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (112 records, 4 fields): 1 millis CompletedMACS2peakCalling