Job ID = 6507828 SRX = SRX494832 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:58:12 prefetch.2.10.7: 1) Downloading 'SRR1198364'... 2020-06-26T13:58:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:01:21 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:01:21 prefetch.2.10.7: 1) 'SRR1198364' was downloaded successfully Read 21509609 spots for SRR1198364/SRR1198364.sra Written 21509609 spots for SRR1198364/SRR1198364.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: 00:05:18 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 255383 (1.19%) aligned 0 times 17821409 (82.85%) aligned exactly 1 time 3432817 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:05:18 Overall time: 00:05:18 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] 3667521 / 21254226 = 0.1726 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 23:13:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.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 23:13:09: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:13:09: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:13:15: 1000000 INFO @ Fri, 26 Jun 2020 23:13:21: 2000000 INFO @ Fri, 26 Jun 2020 23:13:27: 3000000 INFO @ Fri, 26 Jun 2020 23:13:33: 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 23:13:39: 5000000 INFO @ Fri, 26 Jun 2020 23:13:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.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 23:13:39: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:13:39: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:13:45: 1000000 INFO @ Fri, 26 Jun 2020 23:13:45: 6000000 INFO @ Fri, 26 Jun 2020 23:13:51: 2000000 INFO @ Fri, 26 Jun 2020 23:13:51: 7000000 INFO @ Fri, 26 Jun 2020 23:13:57: 3000000 INFO @ Fri, 26 Jun 2020 23:13:57: 8000000 INFO @ Fri, 26 Jun 2020 23:14:03: 4000000 INFO @ Fri, 26 Jun 2020 23:14:03: 9000000 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 23:14:09: 5000000 INFO @ Fri, 26 Jun 2020 23:14:09: 10000000 INFO @ Fri, 26 Jun 2020 23:14:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.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 23:14:09: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:14:09: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:14:15: 6000000 INFO @ Fri, 26 Jun 2020 23:14:16: 11000000 INFO @ Fri, 26 Jun 2020 23:14:16: 1000000 INFO @ Fri, 26 Jun 2020 23:14:22: 7000000 INFO @ Fri, 26 Jun 2020 23:14:22: 12000000 INFO @ Fri, 26 Jun 2020 23:14:22: 2000000 INFO @ Fri, 26 Jun 2020 23:14:28: 13000000 INFO @ Fri, 26 Jun 2020 23:14:28: 8000000 INFO @ Fri, 26 Jun 2020 23:14:29: 3000000 INFO @ Fri, 26 Jun 2020 23:14:34: 14000000 INFO @ Fri, 26 Jun 2020 23:14:35: 9000000 INFO @ Fri, 26 Jun 2020 23:14:35: 4000000 INFO @ Fri, 26 Jun 2020 23:14:40: 15000000 INFO @ Fri, 26 Jun 2020 23:14:41: 10000000 INFO @ Fri, 26 Jun 2020 23:14:41: 5000000 INFO @ Fri, 26 Jun 2020 23:14:46: 16000000 INFO @ Fri, 26 Jun 2020 23:14:47: 11000000 INFO @ Fri, 26 Jun 2020 23:14:48: 6000000 INFO @ Fri, 26 Jun 2020 23:14:53: 17000000 INFO @ Fri, 26 Jun 2020 23:14:54: 12000000 INFO @ Fri, 26 Jun 2020 23:14:54: 7000000 INFO @ Fri, 26 Jun 2020 23:14:56: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 23:14:56: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 23:14:56: #1 total tags in treatment: 17586705 INFO @ Fri, 26 Jun 2020 23:14:56: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:14:56: #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 23:14:57: #1 tags after filtering in treatment: 17586705 INFO @ Fri, 26 Jun 2020 23:14:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:14:57: #1 finished! INFO @ Fri, 26 Jun 2020 23:14:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:14:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:14:58: #2 number of paired peaks: 213 WARNING @ Fri, 26 Jun 2020 23:14:58: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Fri, 26 Jun 2020 23:14:58: start model_add_line... INFO @ Fri, 26 Jun 2020 23:14:58: start X-correlation... INFO @ Fri, 26 Jun 2020 23:14:58: end of X-cor INFO @ Fri, 26 Jun 2020 23:14:58: #2 finished! INFO @ Fri, 26 Jun 2020 23:14:58: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:14:58: #2 alternative fragment length(s) may be 1,42,597 bps INFO @ Fri, 26 Jun 2020 23:14:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.05_model.r WARNING @ Fri, 26 Jun 2020 23:14:58: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:14:58: #2 You may need to consider one of the other alternative d(s): 1,42,597 WARNING @ Fri, 26 Jun 2020 23:14:58: #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 23:14:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:14:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:15:00: 13000000 INFO @ Fri, 26 Jun 2020 23:15:01: 8000000 INFO @ Fri, 26 Jun 2020 23:15:06: 14000000 INFO @ Fri, 26 Jun 2020 23:15:07: 9000000 INFO @ Fri, 26 Jun 2020 23:15:13: 15000000 INFO @ Fri, 26 Jun 2020 23:15:13: 10000000 INFO @ Fri, 26 Jun 2020 23:15:19: 16000000 INFO @ Fri, 26 Jun 2020 23:15:19: 11000000 INFO @ Fri, 26 Jun 2020 23:15:25: 17000000 INFO @ Fri, 26 Jun 2020 23:15:26: 12000000 INFO @ Fri, 26 Jun 2020 23:15:29: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:15:29: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 23:15:29: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 23:15:29: #1 total tags in treatment: 17586705 INFO @ Fri, 26 Jun 2020 23:15:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:15:29: #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 23:15:29: #1 tags after filtering in treatment: 17586705 INFO @ Fri, 26 Jun 2020 23:15:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:15:29: #1 finished! INFO @ Fri, 26 Jun 2020 23:15:29: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:15:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:15:31: #2 number of paired peaks: 213 WARNING @ Fri, 26 Jun 2020 23:15:31: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Fri, 26 Jun 2020 23:15:31: start model_add_line... INFO @ Fri, 26 Jun 2020 23:15:31: start X-correlation... INFO @ Fri, 26 Jun 2020 23:15:31: end of X-cor INFO @ Fri, 26 Jun 2020 23:15:31: #2 finished! INFO @ Fri, 26 Jun 2020 23:15:31: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:15:31: #2 alternative fragment length(s) may be 1,42,597 bps INFO @ Fri, 26 Jun 2020 23:15:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.10_model.r WARNING @ Fri, 26 Jun 2020 23:15:31: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:15:31: #2 You may need to consider one of the other alternative d(s): 1,42,597 WARNING @ Fri, 26 Jun 2020 23:15:31: #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 23:15:31: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:15:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:15:32: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:15:38: 14000000 INFO @ Fri, 26 Jun 2020 23:15:43: 15000000 INFO @ Fri, 26 Jun 2020 23:15:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:15:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:15:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.05_summits.bed INFO @ Fri, 26 Jun 2020 23:15:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:15:49: 16000000 INFO @ Fri, 26 Jun 2020 23:15:55: 17000000 INFO @ Fri, 26 Jun 2020 23:15:59: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 23:15:59: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 23:15:59: #1 total tags in treatment: 17586705 INFO @ Fri, 26 Jun 2020 23:15:59: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:15:59: #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 23:15:59: #1 tags after filtering in treatment: 17586705 INFO @ Fri, 26 Jun 2020 23:15:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:15:59: #1 finished! INFO @ Fri, 26 Jun 2020 23:15:59: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:15:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:16:00: #2 number of paired peaks: 213 WARNING @ Fri, 26 Jun 2020 23:16:00: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Fri, 26 Jun 2020 23:16:00: start model_add_line... INFO @ Fri, 26 Jun 2020 23:16:01: start X-correlation... INFO @ Fri, 26 Jun 2020 23:16:01: end of X-cor INFO @ Fri, 26 Jun 2020 23:16:01: #2 finished! INFO @ Fri, 26 Jun 2020 23:16:01: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:16:01: #2 alternative fragment length(s) may be 1,42,597 bps INFO @ Fri, 26 Jun 2020 23:16:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.20_model.r WARNING @ Fri, 26 Jun 2020 23:16:01: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:16:01: #2 You may need to consider one of the other alternative d(s): 1,42,597 WARNING @ Fri, 26 Jun 2020 23:16:01: #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 23:16:01: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:16:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:16:03: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:16:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:16:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:16:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.10_summits.bed INFO @ Fri, 26 Jun 2020 23:16:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:16:32: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:16:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:16:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:16:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494832/SRX494832.20_summits.bed INFO @ Fri, 26 Jun 2020 23:16:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling