Job ID = 6507935 SRX = SRX495097 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:29:47 prefetch.2.10.7: 1) Downloading 'SRR1198629'... 2020-06-26T13:29:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:30:43 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:30:43 prefetch.2.10.7: 'SRR1198629' is valid 2020-06-26T13:30:43 prefetch.2.10.7: 1) 'SRR1198629' was downloaded successfully Read 15351480 spots for SRR1198629/SRR1198629.sra Written 15351480 spots for SRR1198629/SRR1198629.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: 00:02:51 15351480 reads; of these: 15351480 (100.00%) were unpaired; of these: 137956 (0.90%) aligned 0 times 12385401 (80.68%) aligned exactly 1 time 2828123 (18.42%) aligned >1 times 99.10% overall alignment rate Time searching: 00:02:51 Overall time: 00:02:51 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 2342265 / 15213524 = 0.1540 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 22:37:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.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 22:37:48: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:37:48: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:37:54: 1000000 INFO @ Fri, 26 Jun 2020 22:37:59: 2000000 INFO @ Fri, 26 Jun 2020 22:38:04: 3000000 INFO @ Fri, 26 Jun 2020 22:38:09: 4000000 INFO @ Fri, 26 Jun 2020 22:38:14: 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 22:38:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.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 22:38:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:38:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:38:20: 6000000 INFO @ Fri, 26 Jun 2020 22:38:24: 1000000 INFO @ Fri, 26 Jun 2020 22:38:25: 7000000 INFO @ Fri, 26 Jun 2020 22:38:29: 2000000 INFO @ Fri, 26 Jun 2020 22:38:31: 8000000 INFO @ Fri, 26 Jun 2020 22:38:35: 3000000 INFO @ Fri, 26 Jun 2020 22:38:36: 9000000 INFO @ Fri, 26 Jun 2020 22:38:40: 4000000 INFO @ Fri, 26 Jun 2020 22:38:42: 10000000 INFO @ Fri, 26 Jun 2020 22:38:45: 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 @ Fri, 26 Jun 2020 22:38:47: 11000000 INFO @ Fri, 26 Jun 2020 22:38:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.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 22:38:48: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:38:48: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:38:51: 6000000 INFO @ Fri, 26 Jun 2020 22:38:53: 12000000 INFO @ Fri, 26 Jun 2020 22:38:54: 1000000 INFO @ Fri, 26 Jun 2020 22:38:56: 7000000 INFO @ Fri, 26 Jun 2020 22:38:58: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:38:58: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:38:58: #1 total tags in treatment: 12871259 INFO @ Fri, 26 Jun 2020 22:38:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:38:58: #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 22:38:58: #1 tags after filtering in treatment: 12871259 INFO @ Fri, 26 Jun 2020 22:38:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:38:58: #1 finished! INFO @ Fri, 26 Jun 2020 22:38:58: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:38:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:38:59: #2 number of paired peaks: 366 WARNING @ Fri, 26 Jun 2020 22:38:59: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Fri, 26 Jun 2020 22:38:59: start model_add_line... INFO @ Fri, 26 Jun 2020 22:38:59: start X-correlation... INFO @ Fri, 26 Jun 2020 22:38:59: end of X-cor INFO @ Fri, 26 Jun 2020 22:38:59: #2 finished! INFO @ Fri, 26 Jun 2020 22:38:59: #2 predicted fragment length is 42 bps INFO @ Fri, 26 Jun 2020 22:38:59: #2 alternative fragment length(s) may be 2,42 bps INFO @ Fri, 26 Jun 2020 22:38:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.05_model.r WARNING @ Fri, 26 Jun 2020 22:38:59: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:38:59: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Fri, 26 Jun 2020 22:38:59: #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 22:38:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:38:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:38:59: 2000000 INFO @ Fri, 26 Jun 2020 22:39:02: 8000000 INFO @ Fri, 26 Jun 2020 22:39:05: 3000000 INFO @ Fri, 26 Jun 2020 22:39:07: 9000000 INFO @ Fri, 26 Jun 2020 22:39:10: 4000000 INFO @ Fri, 26 Jun 2020 22:39:13: 10000000 INFO @ Fri, 26 Jun 2020 22:39:15: 5000000 INFO @ Fri, 26 Jun 2020 22:39:18: 11000000 INFO @ Fri, 26 Jun 2020 22:39:21: 6000000 INFO @ Fri, 26 Jun 2020 22:39:23: 12000000 INFO @ Fri, 26 Jun 2020 22:39:25: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:39:27: 7000000 INFO @ Fri, 26 Jun 2020 22:39:28: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:39:28: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:39:28: #1 total tags in treatment: 12871259 INFO @ Fri, 26 Jun 2020 22:39:28: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:39:28: #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 22:39:28: #1 tags after filtering in treatment: 12871259 INFO @ Fri, 26 Jun 2020 22:39:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:39:28: #1 finished! INFO @ Fri, 26 Jun 2020 22:39:28: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:39:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:39:29: #2 number of paired peaks: 366 WARNING @ Fri, 26 Jun 2020 22:39:29: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Fri, 26 Jun 2020 22:39:29: start model_add_line... INFO @ Fri, 26 Jun 2020 22:39:29: start X-correlation... INFO @ Fri, 26 Jun 2020 22:39:29: end of X-cor INFO @ Fri, 26 Jun 2020 22:39:29: #2 finished! INFO @ Fri, 26 Jun 2020 22:39:29: #2 predicted fragment length is 42 bps INFO @ Fri, 26 Jun 2020 22:39:29: #2 alternative fragment length(s) may be 2,42 bps INFO @ Fri, 26 Jun 2020 22:39:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.10_model.r WARNING @ Fri, 26 Jun 2020 22:39:29: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:39:29: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Fri, 26 Jun 2020 22:39:29: #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 22:39:29: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:39:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:39:32: 8000000 INFO @ Fri, 26 Jun 2020 22:39:37: 9000000 INFO @ Fri, 26 Jun 2020 22:39:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:39:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:39:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.05_summits.bed INFO @ Fri, 26 Jun 2020 22:39:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2246 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:39:43: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:39:48: 11000000 INFO @ Fri, 26 Jun 2020 22:39:53: 12000000 INFO @ Fri, 26 Jun 2020 22:39:55: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:39:57: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:39:57: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:39:57: #1 total tags in treatment: 12871259 INFO @ Fri, 26 Jun 2020 22:39:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:39:57: #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 22:39:58: #1 tags after filtering in treatment: 12871259 INFO @ Fri, 26 Jun 2020 22:39:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:39:58: #1 finished! INFO @ Fri, 26 Jun 2020 22:39:58: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:39:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:39:58: #2 number of paired peaks: 366 WARNING @ Fri, 26 Jun 2020 22:39:58: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Fri, 26 Jun 2020 22:39:58: start model_add_line... INFO @ Fri, 26 Jun 2020 22:39:59: start X-correlation... INFO @ Fri, 26 Jun 2020 22:39:59: end of X-cor INFO @ Fri, 26 Jun 2020 22:39:59: #2 finished! INFO @ Fri, 26 Jun 2020 22:39:59: #2 predicted fragment length is 42 bps INFO @ Fri, 26 Jun 2020 22:39:59: #2 alternative fragment length(s) may be 2,42 bps INFO @ Fri, 26 Jun 2020 22:39:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.20_model.r WARNING @ Fri, 26 Jun 2020 22:39:59: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:39:59: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Fri, 26 Jun 2020 22:39:59: #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 22:39:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:39:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:40:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:40:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:40:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.10_summits.bed INFO @ Fri, 26 Jun 2020 22:40:07: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (629 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:40:24: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:40:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:40:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:40:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495097/SRX495097.20_summits.bed INFO @ Fri, 26 Jun 2020 22:40:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (194 records, 4 fields): 2 millis CompletedMACS2peakCalling