Job ID = 6368957 SRX = SRX7627597 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:39:50 prefetch.2.10.7: 1) Downloading 'SRR10961947'... 2020-06-16T00:39:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:42:43 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:42:43 prefetch.2.10.7: 1) 'SRR10961947' was downloaded successfully Read 25839740 spots for SRR10961947/SRR10961947.sra Written 25839740 spots for SRR10961947/SRR10961947.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: 00:05:54 25839740 reads; of these: 25839740 (100.00%) were unpaired; of these: 1337170 (5.17%) aligned 0 times 18061414 (69.90%) aligned exactly 1 time 6441156 (24.93%) aligned >1 times 94.83% overall alignment rate Time searching: 00:05:54 Overall time: 00:05:54 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] 4109082 / 24502570 = 0.1677 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 09:55:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.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 09:55:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:43: 1000000 INFO @ Tue, 16 Jun 2020 09:55:48: 2000000 INFO @ Tue, 16 Jun 2020 09:55:53: 3000000 INFO @ Tue, 16 Jun 2020 09:55:58: 4000000 INFO @ Tue, 16 Jun 2020 09:56:04: 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 @ Tue, 16 Jun 2020 09:56:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.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 09:56:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:56:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:56:09: 6000000 INFO @ Tue, 16 Jun 2020 09:56:12: 1000000 INFO @ Tue, 16 Jun 2020 09:56:14: 7000000 INFO @ Tue, 16 Jun 2020 09:56:17: 2000000 INFO @ Tue, 16 Jun 2020 09:56:20: 8000000 INFO @ Tue, 16 Jun 2020 09:56:22: 3000000 INFO @ Tue, 16 Jun 2020 09:56:25: 9000000 INFO @ Tue, 16 Jun 2020 09:56:26: 4000000 INFO @ Tue, 16 Jun 2020 09:56:30: 10000000 INFO @ Tue, 16 Jun 2020 09:56:31: 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 @ Tue, 16 Jun 2020 09:56:36: 11000000 INFO @ Tue, 16 Jun 2020 09:56:36: 6000000 INFO @ Tue, 16 Jun 2020 09:56:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.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 09:56:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:56:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:56:41: 7000000 INFO @ Tue, 16 Jun 2020 09:56:41: 12000000 INFO @ Tue, 16 Jun 2020 09:56:42: 1000000 INFO @ Tue, 16 Jun 2020 09:56:45: 8000000 INFO @ Tue, 16 Jun 2020 09:56:46: 13000000 INFO @ Tue, 16 Jun 2020 09:56:48: 2000000 INFO @ Tue, 16 Jun 2020 09:56:50: 9000000 INFO @ Tue, 16 Jun 2020 09:56:52: 14000000 INFO @ Tue, 16 Jun 2020 09:56:53: 3000000 INFO @ Tue, 16 Jun 2020 09:56:55: 10000000 INFO @ Tue, 16 Jun 2020 09:56:57: 15000000 INFO @ Tue, 16 Jun 2020 09:56:59: 4000000 INFO @ Tue, 16 Jun 2020 09:57:00: 11000000 INFO @ Tue, 16 Jun 2020 09:57:03: 16000000 INFO @ Tue, 16 Jun 2020 09:57:04: 5000000 INFO @ Tue, 16 Jun 2020 09:57:04: 12000000 INFO @ Tue, 16 Jun 2020 09:57:08: 17000000 INFO @ Tue, 16 Jun 2020 09:57:09: 13000000 INFO @ Tue, 16 Jun 2020 09:57:09: 6000000 INFO @ Tue, 16 Jun 2020 09:57:13: 18000000 INFO @ Tue, 16 Jun 2020 09:57:14: 14000000 INFO @ Tue, 16 Jun 2020 09:57:15: 7000000 INFO @ Tue, 16 Jun 2020 09:57:18: 15000000 INFO @ Tue, 16 Jun 2020 09:57:19: 19000000 INFO @ Tue, 16 Jun 2020 09:57:20: 8000000 INFO @ Tue, 16 Jun 2020 09:57:23: 16000000 INFO @ Tue, 16 Jun 2020 09:57:24: 20000000 INFO @ Tue, 16 Jun 2020 09:57:25: 9000000 INFO @ Tue, 16 Jun 2020 09:57:26: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:57:26: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:57:26: #1 total tags in treatment: 20393488 INFO @ Tue, 16 Jun 2020 09:57:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:57:26: #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 09:57:27: #1 tags after filtering in treatment: 20393488 INFO @ Tue, 16 Jun 2020 09:57:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:57:27: #1 finished! INFO @ Tue, 16 Jun 2020 09:57:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:57:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:57:28: 17000000 INFO @ Tue, 16 Jun 2020 09:57:28: #2 number of paired peaks: 393 WARNING @ Tue, 16 Jun 2020 09:57:28: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Tue, 16 Jun 2020 09:57:28: start model_add_line... INFO @ Tue, 16 Jun 2020 09:57:28: start X-correlation... INFO @ Tue, 16 Jun 2020 09:57:28: end of X-cor INFO @ Tue, 16 Jun 2020 09:57:28: #2 finished! INFO @ Tue, 16 Jun 2020 09:57:28: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:57:28: #2 alternative fragment length(s) may be 1,33 bps INFO @ Tue, 16 Jun 2020 09:57:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.05_model.r WARNING @ Tue, 16 Jun 2020 09:57:28: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:57:28: #2 You may need to consider one of the other alternative d(s): 1,33 WARNING @ Tue, 16 Jun 2020 09:57:28: #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 09:57:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:57:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:57:31: 10000000 INFO @ Tue, 16 Jun 2020 09:57:32: 18000000 INFO @ Tue, 16 Jun 2020 09:57:36: 11000000 INFO @ Tue, 16 Jun 2020 09:57:37: 19000000 INFO @ Tue, 16 Jun 2020 09:57:42: 12000000 INFO @ Tue, 16 Jun 2020 09:57:42: 20000000 INFO @ Tue, 16 Jun 2020 09:57:44: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:57:44: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:57:44: #1 total tags in treatment: 20393488 INFO @ Tue, 16 Jun 2020 09:57:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:57:44: #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 09:57:44: #1 tags after filtering in treatment: 20393488 INFO @ Tue, 16 Jun 2020 09:57:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:57:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:57:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:57:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:57:45: #2 number of paired peaks: 393 WARNING @ Tue, 16 Jun 2020 09:57:45: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Tue, 16 Jun 2020 09:57:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:57:45: start X-correlation... INFO @ Tue, 16 Jun 2020 09:57:45: end of X-cor INFO @ Tue, 16 Jun 2020 09:57:45: #2 finished! INFO @ Tue, 16 Jun 2020 09:57:45: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:57:45: #2 alternative fragment length(s) may be 1,33 bps INFO @ Tue, 16 Jun 2020 09:57:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.10_model.r WARNING @ Tue, 16 Jun 2020 09:57:45: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:57:45: #2 You may need to consider one of the other alternative d(s): 1,33 WARNING @ Tue, 16 Jun 2020 09:57:45: #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 09:57:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:57:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:57:47: 13000000 INFO @ Tue, 16 Jun 2020 09:57:52: 14000000 INFO @ Tue, 16 Jun 2020 09:57:57: 15000000 INFO @ Tue, 16 Jun 2020 09:57:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:58:03: 16000000 INFO @ Tue, 16 Jun 2020 09:58:08: 17000000 INFO @ Tue, 16 Jun 2020 09:58:13: 18000000 INFO @ Tue, 16 Jun 2020 09:58:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:58:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:58:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.05_summits.bed INFO @ Tue, 16 Jun 2020 09:58:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:58:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:58:19: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:58:24: 20000000 INFO @ Tue, 16 Jun 2020 09:58:26: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:58:26: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:58:26: #1 total tags in treatment: 20393488 INFO @ Tue, 16 Jun 2020 09:58:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:58:26: #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 09:58:27: #1 tags after filtering in treatment: 20393488 INFO @ Tue, 16 Jun 2020 09:58:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:58:27: #1 finished! INFO @ Tue, 16 Jun 2020 09:58:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:58:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:58:28: #2 number of paired peaks: 393 WARNING @ Tue, 16 Jun 2020 09:58:28: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Tue, 16 Jun 2020 09:58:28: start model_add_line... INFO @ Tue, 16 Jun 2020 09:58:28: start X-correlation... INFO @ Tue, 16 Jun 2020 09:58:28: end of X-cor INFO @ Tue, 16 Jun 2020 09:58:28: #2 finished! INFO @ Tue, 16 Jun 2020 09:58:28: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:58:28: #2 alternative fragment length(s) may be 1,33 bps INFO @ Tue, 16 Jun 2020 09:58:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.20_model.r WARNING @ Tue, 16 Jun 2020 09:58:28: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:58:28: #2 You may need to consider one of the other alternative d(s): 1,33 WARNING @ Tue, 16 Jun 2020 09:58:28: #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 09:58:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:58:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:58:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:58:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:58:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.10_summits.bed INFO @ Tue, 16 Jun 2020 09:58:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:58:59: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:59:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:59:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:59:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7627597/SRX7627597.20_summits.bed INFO @ Tue, 16 Jun 2020 09:59:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling