Job ID = 6497512 SRX = SRX495102 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:18:59 prefetch.2.10.7: 1) Downloading 'SRR1198634'... 2020-06-25T22:18:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:21:53 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:21:53 prefetch.2.10.7: 1) 'SRR1198634' was downloaded successfully Read 10727987 spots for SRR1198634/SRR1198634.sra Written 10727987 spots for SRR1198634/SRR1198634.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: 00:01:50 10727987 reads; of these: 10727987 (100.00%) were unpaired; of these: 2100085 (19.58%) aligned 0 times 7379740 (68.79%) aligned exactly 1 time 1248162 (11.63%) aligned >1 times 80.42% overall alignment rate Time searching: 00:01:50 Overall time: 00:01:50 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] 1364506 / 8627902 = 0.1582 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 07:27:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.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 @ Fri, 26 Jun 2020 07:27:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:27:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:27:25: 1000000 INFO @ Fri, 26 Jun 2020 07:27:30: 2000000 INFO @ Fri, 26 Jun 2020 07:27:35: 3000000 INFO @ Fri, 26 Jun 2020 07:27:41: 4000000 INFO @ Fri, 26 Jun 2020 07:27:46: 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 @ Fri, 26 Jun 2020 07:27:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.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 @ Fri, 26 Jun 2020 07:27:50: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:27:50: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:27:51: 6000000 INFO @ Fri, 26 Jun 2020 07:27:56: 1000000 INFO @ Fri, 26 Jun 2020 07:27:57: 7000000 INFO @ Fri, 26 Jun 2020 07:27:58: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:27:58: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:27:58: #1 total tags in treatment: 7263396 INFO @ Fri, 26 Jun 2020 07:27:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:27:58: #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 07:27:58: #1 tags after filtering in treatment: 7263396 INFO @ Fri, 26 Jun 2020 07:27:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:27:58: #1 finished! INFO @ Fri, 26 Jun 2020 07:27:58: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:27:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:27:59: #2 number of paired peaks: 312 WARNING @ Fri, 26 Jun 2020 07:27:59: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Fri, 26 Jun 2020 07:27:59: start model_add_line... INFO @ Fri, 26 Jun 2020 07:27:59: start X-correlation... INFO @ Fri, 26 Jun 2020 07:27:59: end of X-cor INFO @ Fri, 26 Jun 2020 07:27:59: #2 finished! INFO @ Fri, 26 Jun 2020 07:27:59: #2 predicted fragment length is 40 bps INFO @ Fri, 26 Jun 2020 07:27:59: #2 alternative fragment length(s) may be 3,40,531,565 bps INFO @ Fri, 26 Jun 2020 07:27:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.05_model.r WARNING @ Fri, 26 Jun 2020 07:27:59: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:27:59: #2 You may need to consider one of the other alternative d(s): 3,40,531,565 WARNING @ Fri, 26 Jun 2020 07:27:59: #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 07:27:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:27:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:28:02: 2000000 INFO @ Fri, 26 Jun 2020 07:28:08: 3000000 INFO @ Fri, 26 Jun 2020 07:28:14: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:28:15: 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 07:28:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.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 @ Fri, 26 Jun 2020 07:28:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:28:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:28:21: 5000000 INFO @ Fri, 26 Jun 2020 07:28:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:28:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:28:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.05_summits.bed INFO @ Fri, 26 Jun 2020 07:28:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (486 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:28:26: 1000000 INFO @ Fri, 26 Jun 2020 07:28:27: 6000000 INFO @ Fri, 26 Jun 2020 07:28:33: 2000000 INFO @ Fri, 26 Jun 2020 07:28:33: 7000000 INFO @ Fri, 26 Jun 2020 07:28:35: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:28:35: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:28:35: #1 total tags in treatment: 7263396 INFO @ Fri, 26 Jun 2020 07:28:35: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:28:35: #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 07:28:35: #1 tags after filtering in treatment: 7263396 INFO @ Fri, 26 Jun 2020 07:28:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:28:35: #1 finished! INFO @ Fri, 26 Jun 2020 07:28:35: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:28:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:28:36: #2 number of paired peaks: 312 WARNING @ Fri, 26 Jun 2020 07:28:36: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Fri, 26 Jun 2020 07:28:36: start model_add_line... INFO @ Fri, 26 Jun 2020 07:28:36: start X-correlation... INFO @ Fri, 26 Jun 2020 07:28:36: end of X-cor INFO @ Fri, 26 Jun 2020 07:28:36: #2 finished! INFO @ Fri, 26 Jun 2020 07:28:36: #2 predicted fragment length is 40 bps INFO @ Fri, 26 Jun 2020 07:28:36: #2 alternative fragment length(s) may be 3,40,531,565 bps INFO @ Fri, 26 Jun 2020 07:28:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.10_model.r WARNING @ Fri, 26 Jun 2020 07:28:36: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:28:36: #2 You may need to consider one of the other alternative d(s): 3,40,531,565 WARNING @ Fri, 26 Jun 2020 07:28:36: #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 07:28:36: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:28:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:28:39: 3000000 INFO @ Fri, 26 Jun 2020 07:28:45: 4000000 INFO @ Fri, 26 Jun 2020 07:28:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:28:51: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:28:57: 6000000 INFO @ Fri, 26 Jun 2020 07:28:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:28:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:28:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.10_summits.bed INFO @ Fri, 26 Jun 2020 07:28:59: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (266 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:29:03: 7000000 INFO @ Fri, 26 Jun 2020 07:29:05: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:29:05: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:29:05: #1 total tags in treatment: 7263396 INFO @ Fri, 26 Jun 2020 07:29:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:29:05: #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 07:29:05: #1 tags after filtering in treatment: 7263396 INFO @ Fri, 26 Jun 2020 07:29:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:29:05: #1 finished! INFO @ Fri, 26 Jun 2020 07:29:05: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:29:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:29:05: #2 number of paired peaks: 312 WARNING @ Fri, 26 Jun 2020 07:29:05: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Fri, 26 Jun 2020 07:29:05: start model_add_line... INFO @ Fri, 26 Jun 2020 07:29:05: start X-correlation... INFO @ Fri, 26 Jun 2020 07:29:05: end of X-cor INFO @ Fri, 26 Jun 2020 07:29:05: #2 finished! INFO @ Fri, 26 Jun 2020 07:29:05: #2 predicted fragment length is 40 bps INFO @ Fri, 26 Jun 2020 07:29:05: #2 alternative fragment length(s) may be 3,40,531,565 bps INFO @ Fri, 26 Jun 2020 07:29:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.20_model.r WARNING @ Fri, 26 Jun 2020 07:29:05: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:29:05: #2 You may need to consider one of the other alternative d(s): 3,40,531,565 WARNING @ Fri, 26 Jun 2020 07:29:05: #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 07:29:05: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:29:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:29:21: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:29:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:29:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:29:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495102/SRX495102.20_summits.bed INFO @ Fri, 26 Jun 2020 07:29:33: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (84 records, 4 fields): 2 millis CompletedMACS2peakCalling