Job ID = 6368732 SRX = SRX5402756 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:28:51 prefetch.2.10.7: 1) Downloading 'SRR8602990'... 2020-06-16T00:28:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:33:29 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:33:29 prefetch.2.10.7: 1) 'SRR8602990' was downloaded successfully Read 31509090 spots for SRR8602990/SRR8602990.sra Written 31509090 spots for SRR8602990/SRR8602990.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: 00:07:10 31509090 reads; of these: 31509090 (100.00%) were unpaired; of these: 2631613 (8.35%) aligned 0 times 23989336 (76.13%) aligned exactly 1 time 4888141 (15.51%) aligned >1 times 91.65% overall alignment rate Time searching: 00:07:10 Overall time: 00:07:10 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] 4404568 / 28877477 = 0.1525 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 09:49:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.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 09:49:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:34: 1000000 INFO @ Tue, 16 Jun 2020 09:49:39: 2000000 INFO @ Tue, 16 Jun 2020 09:49:44: 3000000 INFO @ Tue, 16 Jun 2020 09:49:49: 4000000 INFO @ Tue, 16 Jun 2020 09:49:54: 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 09:49:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.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 09:49:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:00: 6000000 INFO @ Tue, 16 Jun 2020 09:50:04: 1000000 INFO @ Tue, 16 Jun 2020 09:50:05: 7000000 INFO @ Tue, 16 Jun 2020 09:50:09: 2000000 INFO @ Tue, 16 Jun 2020 09:50:10: 8000000 INFO @ Tue, 16 Jun 2020 09:50:14: 3000000 INFO @ Tue, 16 Jun 2020 09:50:15: 9000000 INFO @ Tue, 16 Jun 2020 09:50:20: 4000000 INFO @ Tue, 16 Jun 2020 09:50:20: 10000000 INFO @ Tue, 16 Jun 2020 09:50:25: 5000000 INFO @ Tue, 16 Jun 2020 09:50:25: 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 @ Tue, 16 Jun 2020 09:50:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.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 09:50:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:30: 6000000 INFO @ Tue, 16 Jun 2020 09:50:30: 12000000 INFO @ Tue, 16 Jun 2020 09:50:34: 1000000 INFO @ Tue, 16 Jun 2020 09:50:35: 7000000 INFO @ Tue, 16 Jun 2020 09:50:36: 13000000 INFO @ Tue, 16 Jun 2020 09:50:40: 2000000 INFO @ Tue, 16 Jun 2020 09:50:41: 8000000 INFO @ Tue, 16 Jun 2020 09:50:41: 14000000 INFO @ Tue, 16 Jun 2020 09:50:45: 3000000 INFO @ Tue, 16 Jun 2020 09:50:46: 9000000 INFO @ Tue, 16 Jun 2020 09:50:46: 15000000 INFO @ Tue, 16 Jun 2020 09:50:50: 4000000 INFO @ Tue, 16 Jun 2020 09:50:51: 16000000 INFO @ Tue, 16 Jun 2020 09:50:51: 10000000 INFO @ Tue, 16 Jun 2020 09:50:56: 5000000 INFO @ Tue, 16 Jun 2020 09:50:56: 17000000 INFO @ Tue, 16 Jun 2020 09:50:57: 11000000 INFO @ Tue, 16 Jun 2020 09:51:01: 6000000 INFO @ Tue, 16 Jun 2020 09:51:01: 18000000 INFO @ Tue, 16 Jun 2020 09:51:02: 12000000 INFO @ Tue, 16 Jun 2020 09:51:06: 7000000 INFO @ Tue, 16 Jun 2020 09:51:06: 19000000 INFO @ Tue, 16 Jun 2020 09:51:07: 13000000 INFO @ Tue, 16 Jun 2020 09:51:11: 20000000 INFO @ Tue, 16 Jun 2020 09:51:12: 8000000 INFO @ Tue, 16 Jun 2020 09:51:13: 14000000 INFO @ Tue, 16 Jun 2020 09:51:16: 21000000 INFO @ Tue, 16 Jun 2020 09:51:17: 9000000 INFO @ Tue, 16 Jun 2020 09:51:18: 15000000 INFO @ Tue, 16 Jun 2020 09:51:22: 22000000 INFO @ Tue, 16 Jun 2020 09:51:23: 10000000 INFO @ Tue, 16 Jun 2020 09:51:24: 16000000 INFO @ Tue, 16 Jun 2020 09:51:27: 23000000 INFO @ Tue, 16 Jun 2020 09:51:28: 11000000 INFO @ Tue, 16 Jun 2020 09:51:29: 17000000 INFO @ Tue, 16 Jun 2020 09:51:32: 24000000 INFO @ Tue, 16 Jun 2020 09:51:33: 12000000 INFO @ Tue, 16 Jun 2020 09:51:34: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:51:34: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:51:34: #1 total tags in treatment: 24472909 INFO @ Tue, 16 Jun 2020 09:51:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:34: #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 09:51:34: 18000000 INFO @ Tue, 16 Jun 2020 09:51:35: #1 tags after filtering in treatment: 24472909 INFO @ Tue, 16 Jun 2020 09:51:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:51:35: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:36: #2 number of paired peaks: 122 WARNING @ Tue, 16 Jun 2020 09:51:36: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 16 Jun 2020 09:51:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:36: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:36: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:36: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:51:36: #2 alternative fragment length(s) may be 1,42,459,484,573 bps INFO @ Tue, 16 Jun 2020 09:51:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.05_model.r WARNING @ Tue, 16 Jun 2020 09:51:36: #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 09:51:36: #2 You may need to consider one of the other alternative d(s): 1,42,459,484,573 WARNING @ Tue, 16 Jun 2020 09:51:36: #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 09:51:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:51:38: 13000000 INFO @ Tue, 16 Jun 2020 09:51:40: 19000000 INFO @ Tue, 16 Jun 2020 09:51:43: 14000000 INFO @ Tue, 16 Jun 2020 09:51:45: 20000000 INFO @ Tue, 16 Jun 2020 09:51:49: 15000000 INFO @ Tue, 16 Jun 2020 09:51:50: 21000000 INFO @ Tue, 16 Jun 2020 09:51:54: 16000000 INFO @ Tue, 16 Jun 2020 09:51:55: 22000000 INFO @ Tue, 16 Jun 2020 09:51:59: 17000000 INFO @ Tue, 16 Jun 2020 09:52:01: 23000000 INFO @ Tue, 16 Jun 2020 09:52:04: 18000000 INFO @ Tue, 16 Jun 2020 09:52:06: 24000000 INFO @ Tue, 16 Jun 2020 09:52:09: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:52:09: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:52:09: #1 total tags in treatment: 24472909 INFO @ Tue, 16 Jun 2020 09:52:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:09: #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 09:52:09: #1 tags after filtering in treatment: 24472909 INFO @ Tue, 16 Jun 2020 09:52:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:09: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:09: 19000000 INFO @ Tue, 16 Jun 2020 09:52:11: #2 number of paired peaks: 122 WARNING @ Tue, 16 Jun 2020 09:52:11: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 16 Jun 2020 09:52:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:11: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:52:11: #2 alternative fragment length(s) may be 1,42,459,484,573 bps INFO @ Tue, 16 Jun 2020 09:52:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.10_model.r WARNING @ Tue, 16 Jun 2020 09:52:11: #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 09:52:11: #2 You may need to consider one of the other alternative d(s): 1,42,459,484,573 WARNING @ Tue, 16 Jun 2020 09:52:11: #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 09:52:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:12: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:52:14: 20000000 INFO @ Tue, 16 Jun 2020 09:52:19: 21000000 INFO @ Tue, 16 Jun 2020 09:52:25: 22000000 INFO @ Tue, 16 Jun 2020 09:52:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.05_summits.bed INFO @ Tue, 16 Jun 2020 09:52:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:52:29: 23000000 INFO @ Tue, 16 Jun 2020 09:52:34: 24000000 INFO @ Tue, 16 Jun 2020 09:52:37: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:52:37: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:52:37: #1 total tags in treatment: 24472909 INFO @ Tue, 16 Jun 2020 09:52:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:37: #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 09:52:37: #1 tags after filtering in treatment: 24472909 INFO @ Tue, 16 Jun 2020 09:52:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:39: #2 number of paired peaks: 122 WARNING @ Tue, 16 Jun 2020 09:52:39: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 16 Jun 2020 09:52:39: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:39: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:39: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:39: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:39: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:52:39: #2 alternative fragment length(s) may be 1,42,459,484,573 bps INFO @ Tue, 16 Jun 2020 09:52:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.20_model.r WARNING @ Tue, 16 Jun 2020 09:52:39: #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 09:52:39: #2 You may need to consider one of the other alternative d(s): 1,42,459,484,573 WARNING @ Tue, 16 Jun 2020 09:52:39: #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 09:52:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.10_summits.bed INFO @ Tue, 16 Jun 2020 09:53:03: 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 @ Tue, 16 Jun 2020 09:53:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402756/SRX5402756.20_summits.bed INFO @ Tue, 16 Jun 2020 09:53:31: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling