Job ID = 6497503 SRX = SRX495024 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:54:13 prefetch.2.10.7: 1) Downloading 'SRR1198556'... 2020-06-25T22:54:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:56:16 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:56:16 prefetch.2.10.7: 1) 'SRR1198556' was downloaded successfully Read 11722131 spots for SRR1198556/SRR1198556.sra Written 11722131 spots for SRR1198556/SRR1198556.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: 00:02:11 11722131 reads; of these: 11722131 (100.00%) were unpaired; of these: 1483144 (12.65%) aligned 0 times 8456732 (72.14%) aligned exactly 1 time 1782255 (15.20%) aligned >1 times 87.35% overall alignment rate Time searching: 00:02:11 Overall time: 00:02:11 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] 3217807 / 10238987 = 0.3143 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 08:01:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.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 08:01:40: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:01:40: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:01:46: 1000000 INFO @ Fri, 26 Jun 2020 08:01:53: 2000000 INFO @ Fri, 26 Jun 2020 08:01:59: 3000000 INFO @ Fri, 26 Jun 2020 08:02:05: 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 08:02:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.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 08:02:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:02:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:02:11: 5000000 INFO @ Fri, 26 Jun 2020 08:02:17: 1000000 INFO @ Fri, 26 Jun 2020 08:02:17: 6000000 INFO @ Fri, 26 Jun 2020 08:02:23: 2000000 INFO @ Fri, 26 Jun 2020 08:02:24: 7000000 INFO @ Fri, 26 Jun 2020 08:02:24: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 08:02:24: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 08:02:24: #1 total tags in treatment: 7021180 INFO @ Fri, 26 Jun 2020 08:02:24: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:02:24: #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 08:02:24: #1 tags after filtering in treatment: 7021180 INFO @ Fri, 26 Jun 2020 08:02:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:02:24: #1 finished! INFO @ Fri, 26 Jun 2020 08:02:24: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:02:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:02:25: #2 number of paired peaks: 436 WARNING @ Fri, 26 Jun 2020 08:02:25: Fewer paired peaks (436) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 436 pairs to build model! INFO @ Fri, 26 Jun 2020 08:02:25: start model_add_line... INFO @ Fri, 26 Jun 2020 08:02:25: start X-correlation... INFO @ Fri, 26 Jun 2020 08:02:25: end of X-cor INFO @ Fri, 26 Jun 2020 08:02:25: #2 finished! INFO @ Fri, 26 Jun 2020 08:02:25: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 08:02:25: #2 alternative fragment length(s) may be 4,49,62 bps INFO @ Fri, 26 Jun 2020 08:02:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.05_model.r WARNING @ Fri, 26 Jun 2020 08:02:25: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:02:25: #2 You may need to consider one of the other alternative d(s): 4,49,62 WARNING @ Fri, 26 Jun 2020 08:02:25: #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 08:02:25: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:02:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:02:29: 3000000 INFO @ Fri, 26 Jun 2020 08:02:35: 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 08:02:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.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 08:02:40: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:02:40: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:02:41: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:02:42: 5000000 INFO @ Fri, 26 Jun 2020 08:02:48: 1000000 INFO @ Fri, 26 Jun 2020 08:02:49: 6000000 INFO @ Fri, 26 Jun 2020 08:02:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:02:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:02:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.05_summits.bed INFO @ Fri, 26 Jun 2020 08:02:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (745 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:02:56: 7000000 INFO @ Fri, 26 Jun 2020 08:02:56: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 08:02:56: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 08:02:56: #1 total tags in treatment: 7021180 INFO @ Fri, 26 Jun 2020 08:02:56: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:02:56: #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 08:02:56: #1 tags after filtering in treatment: 7021180 INFO @ Fri, 26 Jun 2020 08:02:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:02:56: #1 finished! INFO @ Fri, 26 Jun 2020 08:02:56: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:02:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:02:56: 2000000 INFO @ Fri, 26 Jun 2020 08:02:56: #2 number of paired peaks: 436 WARNING @ Fri, 26 Jun 2020 08:02:56: Fewer paired peaks (436) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 436 pairs to build model! INFO @ Fri, 26 Jun 2020 08:02:56: start model_add_line... INFO @ Fri, 26 Jun 2020 08:02:56: start X-correlation... INFO @ Fri, 26 Jun 2020 08:02:56: end of X-cor INFO @ Fri, 26 Jun 2020 08:02:56: #2 finished! INFO @ Fri, 26 Jun 2020 08:02:56: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 08:02:56: #2 alternative fragment length(s) may be 4,49,62 bps INFO @ Fri, 26 Jun 2020 08:02:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.10_model.r WARNING @ Fri, 26 Jun 2020 08:02:56: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:02:56: #2 You may need to consider one of the other alternative d(s): 4,49,62 WARNING @ Fri, 26 Jun 2020 08:02:56: #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 08:02:56: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:02:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:03:03: 3000000 INFO @ Fri, 26 Jun 2020 08:03:10: 4000000 INFO @ Fri, 26 Jun 2020 08:03:13: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:03:17: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:03:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:03:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:03:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.10_summits.bed INFO @ Fri, 26 Jun 2020 08:03:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (395 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:03:24: 6000000 INFO @ Fri, 26 Jun 2020 08:03:31: 7000000 INFO @ Fri, 26 Jun 2020 08:03:31: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 08:03:31: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 08:03:31: #1 total tags in treatment: 7021180 INFO @ Fri, 26 Jun 2020 08:03:31: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:03:31: #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 08:03:32: #1 tags after filtering in treatment: 7021180 INFO @ Fri, 26 Jun 2020 08:03:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:03:32: #1 finished! INFO @ Fri, 26 Jun 2020 08:03:32: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:03:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:03:32: #2 number of paired peaks: 436 WARNING @ Fri, 26 Jun 2020 08:03:32: Fewer paired peaks (436) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 436 pairs to build model! INFO @ Fri, 26 Jun 2020 08:03:32: start model_add_line... INFO @ Fri, 26 Jun 2020 08:03:32: start X-correlation... INFO @ Fri, 26 Jun 2020 08:03:32: end of X-cor INFO @ Fri, 26 Jun 2020 08:03:32: #2 finished! INFO @ Fri, 26 Jun 2020 08:03:32: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 08:03:32: #2 alternative fragment length(s) may be 4,49,62 bps INFO @ Fri, 26 Jun 2020 08:03:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.20_model.r WARNING @ Fri, 26 Jun 2020 08:03:32: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:03:32: #2 You may need to consider one of the other alternative d(s): 4,49,62 WARNING @ Fri, 26 Jun 2020 08:03:32: #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 08:03:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:03:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:03:48: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:03:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:03:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:03:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495024/SRX495024.20_summits.bed INFO @ Fri, 26 Jun 2020 08:03:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (156 records, 4 fields): 1 millis CompletedMACS2peakCalling