Job ID = 6369018 SRX = SRX982084 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:50:40 prefetch.2.10.7: 1) Downloading 'SRR1956571'... 2020-06-16T00:50:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:51:51 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:51:51 prefetch.2.10.7: 'SRR1956571' is valid 2020-06-16T00:51:51 prefetch.2.10.7: 1) 'SRR1956571' was downloaded successfully Read 11041038 spots for SRR1956571/SRR1956571.sra Written 11041038 spots for SRR1956571/SRR1956571.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: 00:02:21 11041038 reads; of these: 11041038 (100.00%) were unpaired; of these: 1167750 (10.58%) aligned 0 times 8131831 (73.65%) aligned exactly 1 time 1741457 (15.77%) aligned >1 times 89.42% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 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_sort_core] merging from 8 files... [bam_rmdupse_core] 913481 / 9873288 = 0.0925 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 09:57:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.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 09:57:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:57:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:57:54: 1000000 INFO @ Tue, 16 Jun 2020 09:58:01: 2000000 INFO @ Tue, 16 Jun 2020 09:58:08: 3000000 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 09:58:15: 4000000 INFO @ Tue, 16 Jun 2020 09:58:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.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 09:58:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:58:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:58:23: 5000000 INFO @ Tue, 16 Jun 2020 09:58:24: 1000000 INFO @ Tue, 16 Jun 2020 09:58:31: 6000000 INFO @ Tue, 16 Jun 2020 09:58:33: 2000000 INFO @ Tue, 16 Jun 2020 09:58:39: 7000000 INFO @ Tue, 16 Jun 2020 09:58:41: 3000000 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 09:58:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.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 09:58:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:58:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:58:47: 8000000 INFO @ Tue, 16 Jun 2020 09:58:49: 4000000 INFO @ Tue, 16 Jun 2020 09:58:54: 1000000 INFO @ Tue, 16 Jun 2020 09:58:55: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:58:55: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:58:55: #1 total tags in treatment: 8959807 INFO @ Tue, 16 Jun 2020 09:58:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:58:55: #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 09:58:55: #1 tags after filtering in treatment: 8959807 INFO @ Tue, 16 Jun 2020 09:58:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:58:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:58:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:58:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:58:56: #2 number of paired peaks: 377 WARNING @ Tue, 16 Jun 2020 09:58:56: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Tue, 16 Jun 2020 09:58:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:58:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:58:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:58:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:58:56: #2 predicted fragment length is 58 bps INFO @ Tue, 16 Jun 2020 09:58:56: #2 alternative fragment length(s) may be 4,58 bps INFO @ Tue, 16 Jun 2020 09:58:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.05_model.r WARNING @ Tue, 16 Jun 2020 09:58:56: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:58:56: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Tue, 16 Jun 2020 09:58:56: #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 09:58:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:58:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:58:58: 5000000 INFO @ Tue, 16 Jun 2020 09:59:02: 2000000 INFO @ Tue, 16 Jun 2020 09:59:06: 6000000 INFO @ Tue, 16 Jun 2020 09:59:09: 3000000 INFO @ Tue, 16 Jun 2020 09:59:14: 7000000 INFO @ Tue, 16 Jun 2020 09:59:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:59:17: 4000000 INFO @ Tue, 16 Jun 2020 09:59:22: 8000000 INFO @ Tue, 16 Jun 2020 09:59:24: 5000000 INFO @ Tue, 16 Jun 2020 09:59:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:59:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:59:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.05_summits.bed INFO @ Tue, 16 Jun 2020 09:59:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (682 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:59:30: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:59:30: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:59:30: #1 total tags in treatment: 8959807 INFO @ Tue, 16 Jun 2020 09:59:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:59:30: #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 09:59:30: #1 tags after filtering in treatment: 8959807 INFO @ Tue, 16 Jun 2020 09:59:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:59:30: #1 finished! INFO @ Tue, 16 Jun 2020 09:59:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:59:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:59:31: #2 number of paired peaks: 377 WARNING @ Tue, 16 Jun 2020 09:59:31: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Tue, 16 Jun 2020 09:59:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:59:31: start X-correlation... INFO @ Tue, 16 Jun 2020 09:59:31: end of X-cor INFO @ Tue, 16 Jun 2020 09:59:31: #2 finished! INFO @ Tue, 16 Jun 2020 09:59:31: #2 predicted fragment length is 58 bps INFO @ Tue, 16 Jun 2020 09:59:31: #2 alternative fragment length(s) may be 4,58 bps INFO @ Tue, 16 Jun 2020 09:59:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.10_model.r WARNING @ Tue, 16 Jun 2020 09:59:31: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:59:31: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Tue, 16 Jun 2020 09:59:31: #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 09:59:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:59:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:59:31: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:59:38: 7000000 INFO @ Tue, 16 Jun 2020 09:59:44: 8000000 INFO @ Tue, 16 Jun 2020 09:59:50: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:59:50: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:59:50: #1 total tags in treatment: 8959807 INFO @ Tue, 16 Jun 2020 09:59:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:59:50: #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 09:59:50: #1 tags after filtering in treatment: 8959807 INFO @ Tue, 16 Jun 2020 09:59:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:59:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:59:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:59:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:59:51: #2 number of paired peaks: 377 WARNING @ Tue, 16 Jun 2020 09:59:51: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Tue, 16 Jun 2020 09:59:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:59:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:59:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:59:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:59:51: #2 predicted fragment length is 58 bps INFO @ Tue, 16 Jun 2020 09:59:51: #2 alternative fragment length(s) may be 4,58 bps INFO @ Tue, 16 Jun 2020 09:59:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.20_model.r WARNING @ Tue, 16 Jun 2020 09:59:51: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:59:51: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Tue, 16 Jun 2020 09:59:51: #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 09:59:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:59:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:59:51: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:00:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:00:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:00:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.10_summits.bed INFO @ Tue, 16 Jun 2020 10:00:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (346 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:00:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:00:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:00:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:00:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982084/SRX982084.20_summits.bed INFO @ Tue, 16 Jun 2020 10:00:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (163 records, 4 fields): 1 millis CompletedMACS2peakCalling