Job ID = 6497504 SRX = SRX495025 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:43:55 prefetch.2.10.7: 1) Downloading 'SRR1198557'... 2020-06-25T21:43:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:46:23 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:46:23 prefetch.2.10.7: 1) 'SRR1198557' was downloaded successfully Read 22970231 spots for SRR1198557/SRR1198557.sra Written 22970231 spots for SRR1198557/SRR1198557.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: 00:04:47 22970231 reads; of these: 22970231 (100.00%) were unpaired; of these: 2517551 (10.96%) aligned 0 times 16805786 (73.16%) aligned exactly 1 time 3646894 (15.88%) aligned >1 times 89.04% overall alignment rate Time searching: 00:04:47 Overall time: 00:04:47 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 12 files... [bam_rmdupse_core] 2296772 / 20452680 = 0.1123 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 06:57:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.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 06:57:41: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:57:41: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:57:46: 1000000 INFO @ Fri, 26 Jun 2020 06:57:51: 2000000 INFO @ Fri, 26 Jun 2020 06:57:56: 3000000 INFO @ Fri, 26 Jun 2020 06:58:01: 4000000 INFO @ Fri, 26 Jun 2020 06:58:06: 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 06:58:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.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 06:58:09: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:58:09: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:58:10: 6000000 INFO @ Fri, 26 Jun 2020 06:58:14: 1000000 INFO @ Fri, 26 Jun 2020 06:58:16: 7000000 INFO @ Fri, 26 Jun 2020 06:58:20: 2000000 INFO @ Fri, 26 Jun 2020 06:58:21: 8000000 INFO @ Fri, 26 Jun 2020 06:58:25: 3000000 INFO @ Fri, 26 Jun 2020 06:58:26: 9000000 INFO @ Fri, 26 Jun 2020 06:58:30: 4000000 INFO @ Fri, 26 Jun 2020 06:58:31: 10000000 INFO @ Fri, 26 Jun 2020 06:58:35: 5000000 INFO @ Fri, 26 Jun 2020 06:58:36: 11000000 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 06:58:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.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 06:58:39: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:58:39: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:58:40: 6000000 INFO @ Fri, 26 Jun 2020 06:58:41: 12000000 INFO @ Fri, 26 Jun 2020 06:58:44: 1000000 INFO @ Fri, 26 Jun 2020 06:58:45: 7000000 INFO @ Fri, 26 Jun 2020 06:58:46: 13000000 INFO @ Fri, 26 Jun 2020 06:58:49: 2000000 INFO @ Fri, 26 Jun 2020 06:58:50: 8000000 INFO @ Fri, 26 Jun 2020 06:58:51: 14000000 INFO @ Fri, 26 Jun 2020 06:58:54: 3000000 INFO @ Fri, 26 Jun 2020 06:58:55: 9000000 INFO @ Fri, 26 Jun 2020 06:58:56: 15000000 INFO @ Fri, 26 Jun 2020 06:58:59: 4000000 INFO @ Fri, 26 Jun 2020 06:59:00: 10000000 INFO @ Fri, 26 Jun 2020 06:59:01: 16000000 INFO @ Fri, 26 Jun 2020 06:59:04: 5000000 INFO @ Fri, 26 Jun 2020 06:59:05: 11000000 INFO @ Fri, 26 Jun 2020 06:59:06: 17000000 INFO @ Fri, 26 Jun 2020 06:59:09: 6000000 INFO @ Fri, 26 Jun 2020 06:59:10: 12000000 INFO @ Fri, 26 Jun 2020 06:59:11: 18000000 INFO @ Fri, 26 Jun 2020 06:59:12: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 06:59:12: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 06:59:12: #1 total tags in treatment: 18155908 INFO @ Fri, 26 Jun 2020 06:59:12: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:59:12: #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 06:59:12: #1 tags after filtering in treatment: 18155908 INFO @ Fri, 26 Jun 2020 06:59:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:59:12: #1 finished! INFO @ Fri, 26 Jun 2020 06:59:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:59:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:59:13: #2 number of paired peaks: 258 WARNING @ Fri, 26 Jun 2020 06:59:13: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Fri, 26 Jun 2020 06:59:13: start model_add_line... INFO @ Fri, 26 Jun 2020 06:59:13: start X-correlation... INFO @ Fri, 26 Jun 2020 06:59:13: end of X-cor INFO @ Fri, 26 Jun 2020 06:59:13: #2 finished! INFO @ Fri, 26 Jun 2020 06:59:13: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 06:59:13: #2 alternative fragment length(s) may be 1,32,572,592 bps INFO @ Fri, 26 Jun 2020 06:59:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.05_model.r WARNING @ Fri, 26 Jun 2020 06:59:13: #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 06:59:13: #2 You may need to consider one of the other alternative d(s): 1,32,572,592 WARNING @ Fri, 26 Jun 2020 06:59:13: #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 06:59:13: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:59:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:59:15: 7000000 INFO @ Fri, 26 Jun 2020 06:59:15: 13000000 INFO @ Fri, 26 Jun 2020 06:59:20: 8000000 INFO @ Fri, 26 Jun 2020 06:59:20: 14000000 INFO @ Fri, 26 Jun 2020 06:59:25: 9000000 INFO @ Fri, 26 Jun 2020 06:59:25: 15000000 INFO @ Fri, 26 Jun 2020 06:59:30: 10000000 INFO @ Fri, 26 Jun 2020 06:59:30: 16000000 INFO @ Fri, 26 Jun 2020 06:59:35: 17000000 INFO @ Fri, 26 Jun 2020 06:59:35: 11000000 INFO @ Fri, 26 Jun 2020 06:59:40: 18000000 INFO @ Fri, 26 Jun 2020 06:59:40: 12000000 INFO @ Fri, 26 Jun 2020 06:59:41: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 06:59:41: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 06:59:41: #1 total tags in treatment: 18155908 INFO @ Fri, 26 Jun 2020 06:59:41: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:59:41: #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 06:59:41: #1 tags after filtering in treatment: 18155908 INFO @ Fri, 26 Jun 2020 06:59:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:59:41: #1 finished! INFO @ Fri, 26 Jun 2020 06:59:41: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:59:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:59:42: #2 number of paired peaks: 258 WARNING @ Fri, 26 Jun 2020 06:59:42: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Fri, 26 Jun 2020 06:59:42: start model_add_line... INFO @ Fri, 26 Jun 2020 06:59:43: start X-correlation... INFO @ Fri, 26 Jun 2020 06:59:43: end of X-cor INFO @ Fri, 26 Jun 2020 06:59:43: #2 finished! INFO @ Fri, 26 Jun 2020 06:59:43: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 06:59:43: #2 alternative fragment length(s) may be 1,32,572,592 bps INFO @ Fri, 26 Jun 2020 06:59:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.10_model.r WARNING @ Fri, 26 Jun 2020 06:59:43: #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 06:59:43: #2 You may need to consider one of the other alternative d(s): 1,32,572,592 WARNING @ Fri, 26 Jun 2020 06:59:43: #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 06:59:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:59:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:59:43: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:59:45: 13000000 INFO @ Fri, 26 Jun 2020 06:59:50: 14000000 INFO @ Fri, 26 Jun 2020 06:59:55: 15000000 INFO @ Fri, 26 Jun 2020 06:59:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.05_peaks.xls INFO @ Fri, 26 Jun 2020 06:59:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:59:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.05_summits.bed INFO @ Fri, 26 Jun 2020 06:59:57: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:00:00: 16000000 INFO @ Fri, 26 Jun 2020 07:00:05: 17000000 INFO @ Fri, 26 Jun 2020 07:00:09: 18000000 INFO @ Fri, 26 Jun 2020 07:00:10: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:00:10: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:00:10: #1 total tags in treatment: 18155908 INFO @ Fri, 26 Jun 2020 07:00:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:00:10: #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 07:00:10: #1 tags after filtering in treatment: 18155908 INFO @ Fri, 26 Jun 2020 07:00:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:00:10: #1 finished! INFO @ Fri, 26 Jun 2020 07:00:10: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:00:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:00:12: #2 number of paired peaks: 258 WARNING @ Fri, 26 Jun 2020 07:00:12: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Fri, 26 Jun 2020 07:00:12: start model_add_line... INFO @ Fri, 26 Jun 2020 07:00:12: start X-correlation... INFO @ Fri, 26 Jun 2020 07:00:12: end of X-cor INFO @ Fri, 26 Jun 2020 07:00:12: #2 finished! INFO @ Fri, 26 Jun 2020 07:00:12: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:00:12: #2 alternative fragment length(s) may be 1,32,572,592 bps INFO @ Fri, 26 Jun 2020 07:00:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.20_model.r WARNING @ Fri, 26 Jun 2020 07:00:12: #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 07:00:12: #2 You may need to consider one of the other alternative d(s): 1,32,572,592 WARNING @ Fri, 26 Jun 2020 07:00:12: #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 07:00:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:00:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:00:12: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:00:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:00:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:00:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.10_summits.bed INFO @ Fri, 26 Jun 2020 07:00:26: 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 07:00:42: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:00:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:00:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:00:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495025/SRX495025.20_summits.bed INFO @ Fri, 26 Jun 2020 07:00:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling