Job ID = 6366357 SRX = SRX1299430 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:41:06 prefetch.2.10.7: 1) Downloading 'SRR2545912'... 2020-06-15T22:41:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:42:02 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:42:02 prefetch.2.10.7: 'SRR2545912' is valid 2020-06-15T22:42:02 prefetch.2.10.7: 1) 'SRR2545912' was downloaded successfully Read 11686474 spots for SRR2545912/SRR2545912.sra Written 11686474 spots for SRR2545912/SRR2545912.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: 00:02:27 11686474 reads; of these: 11686474 (100.00%) were unpaired; of these: 2539725 (21.73%) aligned 0 times 7717481 (66.04%) aligned exactly 1 time 1429268 (12.23%) aligned >1 times 78.27% overall alignment rate Time searching: 00:02:27 Overall time: 00:02:27 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] 608262 / 9146749 = 0.0665 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 07:47:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.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 07:47:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:47:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:48:02: 1000000 INFO @ Tue, 16 Jun 2020 07:48:09: 2000000 INFO @ Tue, 16 Jun 2020 07:48:16: 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 07:48:23: 4000000 INFO @ Tue, 16 Jun 2020 07:48:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.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 07:48:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:48:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:48:31: 5000000 INFO @ Tue, 16 Jun 2020 07:48:32: 1000000 INFO @ Tue, 16 Jun 2020 07:48:38: 6000000 INFO @ Tue, 16 Jun 2020 07:48:40: 2000000 INFO @ Tue, 16 Jun 2020 07:48:45: 7000000 INFO @ Tue, 16 Jun 2020 07:48:48: 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 07:48:53: 8000000 INFO @ Tue, 16 Jun 2020 07:48:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.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 07:48:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:48:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:48:55: 4000000 INFO @ Tue, 16 Jun 2020 07:48:57: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:48:57: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:48:57: #1 total tags in treatment: 8538487 INFO @ Tue, 16 Jun 2020 07:48:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:48:57: #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 07:48:57: #1 tags after filtering in treatment: 8538487 INFO @ Tue, 16 Jun 2020 07:48:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:48:57: #1 finished! INFO @ Tue, 16 Jun 2020 07:48:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:48:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:48:57: #2 number of paired peaks: 325 WARNING @ Tue, 16 Jun 2020 07:48:57: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Tue, 16 Jun 2020 07:48:57: start model_add_line... INFO @ Tue, 16 Jun 2020 07:48:57: start X-correlation... INFO @ Tue, 16 Jun 2020 07:48:57: end of X-cor INFO @ Tue, 16 Jun 2020 07:48:57: #2 finished! INFO @ Tue, 16 Jun 2020 07:48:57: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 07:48:57: #2 alternative fragment length(s) may be 4,51,519,545,561 bps INFO @ Tue, 16 Jun 2020 07:48:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.05_model.r WARNING @ Tue, 16 Jun 2020 07:48:57: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:48:57: #2 You may need to consider one of the other alternative d(s): 4,51,519,545,561 WARNING @ Tue, 16 Jun 2020 07:48:57: #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 07:48:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:48:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:49:02: 1000000 INFO @ Tue, 16 Jun 2020 07:49:03: 5000000 INFO @ Tue, 16 Jun 2020 07:49:10: 6000000 INFO @ Tue, 16 Jun 2020 07:49:10: 2000000 INFO @ Tue, 16 Jun 2020 07:49:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:49:17: 7000000 INFO @ Tue, 16 Jun 2020 07:49:19: 3000000 INFO @ Tue, 16 Jun 2020 07:49:25: 8000000 INFO @ Tue, 16 Jun 2020 07:49:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:49:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:49:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.05_summits.bed INFO @ Tue, 16 Jun 2020 07:49:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (546 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:49:27: 4000000 INFO @ Tue, 16 Jun 2020 07:49:28: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:49:28: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:49:28: #1 total tags in treatment: 8538487 INFO @ Tue, 16 Jun 2020 07:49:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:49:28: #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 07:49:28: #1 tags after filtering in treatment: 8538487 INFO @ Tue, 16 Jun 2020 07:49:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:49:28: #1 finished! INFO @ Tue, 16 Jun 2020 07:49:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:49:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:49:29: #2 number of paired peaks: 325 WARNING @ Tue, 16 Jun 2020 07:49:29: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Tue, 16 Jun 2020 07:49:29: start model_add_line... INFO @ Tue, 16 Jun 2020 07:49:29: start X-correlation... INFO @ Tue, 16 Jun 2020 07:49:29: end of X-cor INFO @ Tue, 16 Jun 2020 07:49:29: #2 finished! INFO @ Tue, 16 Jun 2020 07:49:29: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 07:49:29: #2 alternative fragment length(s) may be 4,51,519,545,561 bps INFO @ Tue, 16 Jun 2020 07:49:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.10_model.r WARNING @ Tue, 16 Jun 2020 07:49:29: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:49:29: #2 You may need to consider one of the other alternative d(s): 4,51,519,545,561 WARNING @ Tue, 16 Jun 2020 07:49:29: #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 07:49:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:49:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:49:34: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:49:41: 6000000 INFO @ Tue, 16 Jun 2020 07:49:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:49:49: 7000000 INFO @ Tue, 16 Jun 2020 07:49:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:49:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:49:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.10_summits.bed INFO @ Tue, 16 Jun 2020 07:49:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (357 records, 4 fields): 1 millis INFO @ Tue, 16 Jun 2020 07:49:56: 8000000 CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:50:00: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:50:00: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:50:00: #1 total tags in treatment: 8538487 INFO @ Tue, 16 Jun 2020 07:50:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:50:00: #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 07:50:00: #1 tags after filtering in treatment: 8538487 INFO @ Tue, 16 Jun 2020 07:50:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:50:00: #1 finished! INFO @ Tue, 16 Jun 2020 07:50:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:50:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:50:00: #2 number of paired peaks: 325 WARNING @ Tue, 16 Jun 2020 07:50:00: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Tue, 16 Jun 2020 07:50:00: start model_add_line... INFO @ Tue, 16 Jun 2020 07:50:00: start X-correlation... INFO @ Tue, 16 Jun 2020 07:50:01: end of X-cor INFO @ Tue, 16 Jun 2020 07:50:01: #2 finished! INFO @ Tue, 16 Jun 2020 07:50:01: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 07:50:01: #2 alternative fragment length(s) may be 4,51,519,545,561 bps INFO @ Tue, 16 Jun 2020 07:50:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.20_model.r WARNING @ Tue, 16 Jun 2020 07:50:01: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:50:01: #2 You may need to consider one of the other alternative d(s): 4,51,519,545,561 WARNING @ Tue, 16 Jun 2020 07:50:01: #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 07:50:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:50:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:50:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:50:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:50:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:50:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1299430/SRX1299430.20_summits.bed INFO @ Tue, 16 Jun 2020 07:50:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (153 records, 4 fields): 1 millis CompletedMACS2peakCalling