Job ID = 6368878 SRX = SRX6619575 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:33:09 prefetch.2.10.7: 1) Downloading 'SRR9866034'... 2020-06-16T00:33:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:36:32 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:36:32 prefetch.2.10.7: 1) 'SRR9866034' was downloaded successfully 2020-06-16T00:36:32 prefetch.2.10.7: 'SRR9866034' has 0 unresolved dependencies Read 37437324 spots for SRR9866034/SRR9866034.sra Written 37437324 spots for SRR9866034/SRR9866034.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: 00:08:03 37437324 reads; of these: 37437324 (100.00%) were unpaired; of these: 3098062 (8.28%) aligned 0 times 28631344 (76.48%) aligned exactly 1 time 5707918 (15.25%) aligned >1 times 91.72% overall alignment rate Time searching: 00:08:03 Overall time: 00:08:03 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 16 files... [bam_rmdupse_core] 6995508 / 34339262 = 0.2037 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 09:54:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.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 09:54:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:54:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:54:18: 1000000 INFO @ Tue, 16 Jun 2020 09:54:23: 2000000 INFO @ Tue, 16 Jun 2020 09:54:29: 3000000 INFO @ Tue, 16 Jun 2020 09:54:34: 4000000 INFO @ Tue, 16 Jun 2020 09:54:40: 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 09:54:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.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 09:54:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:54:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:54:45: 6000000 INFO @ Tue, 16 Jun 2020 09:54:48: 1000000 INFO @ Tue, 16 Jun 2020 09:54:51: 7000000 INFO @ Tue, 16 Jun 2020 09:54:53: 2000000 INFO @ Tue, 16 Jun 2020 09:54:56: 8000000 INFO @ Tue, 16 Jun 2020 09:54:59: 3000000 INFO @ Tue, 16 Jun 2020 09:55:02: 9000000 INFO @ Tue, 16 Jun 2020 09:55:05: 4000000 INFO @ Tue, 16 Jun 2020 09:55:08: 10000000 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 09:55:10: 5000000 INFO @ Tue, 16 Jun 2020 09:55:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.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 09:55:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:14: 11000000 INFO @ Tue, 16 Jun 2020 09:55:16: 6000000 INFO @ Tue, 16 Jun 2020 09:55:17: 1000000 INFO @ Tue, 16 Jun 2020 09:55:20: 12000000 INFO @ Tue, 16 Jun 2020 09:55:22: 7000000 INFO @ Tue, 16 Jun 2020 09:55:22: 2000000 INFO @ Tue, 16 Jun 2020 09:55:25: 13000000 INFO @ Tue, 16 Jun 2020 09:55:27: 3000000 INFO @ Tue, 16 Jun 2020 09:55:27: 8000000 INFO @ Tue, 16 Jun 2020 09:55:31: 14000000 INFO @ Tue, 16 Jun 2020 09:55:32: 4000000 INFO @ Tue, 16 Jun 2020 09:55:33: 9000000 INFO @ Tue, 16 Jun 2020 09:55:37: 15000000 INFO @ Tue, 16 Jun 2020 09:55:37: 5000000 INFO @ Tue, 16 Jun 2020 09:55:39: 10000000 INFO @ Tue, 16 Jun 2020 09:55:42: 6000000 INFO @ Tue, 16 Jun 2020 09:55:43: 16000000 INFO @ Tue, 16 Jun 2020 09:55:44: 11000000 INFO @ Tue, 16 Jun 2020 09:55:47: 7000000 INFO @ Tue, 16 Jun 2020 09:55:49: 17000000 INFO @ Tue, 16 Jun 2020 09:55:50: 12000000 INFO @ Tue, 16 Jun 2020 09:55:52: 8000000 INFO @ Tue, 16 Jun 2020 09:55:55: 18000000 INFO @ Tue, 16 Jun 2020 09:55:56: 13000000 INFO @ Tue, 16 Jun 2020 09:55:57: 9000000 INFO @ Tue, 16 Jun 2020 09:56:00: 19000000 INFO @ Tue, 16 Jun 2020 09:56:02: 14000000 INFO @ Tue, 16 Jun 2020 09:56:02: 10000000 INFO @ Tue, 16 Jun 2020 09:56:06: 20000000 INFO @ Tue, 16 Jun 2020 09:56:07: 11000000 INFO @ Tue, 16 Jun 2020 09:56:07: 15000000 INFO @ Tue, 16 Jun 2020 09:56:12: 12000000 INFO @ Tue, 16 Jun 2020 09:56:12: 21000000 INFO @ Tue, 16 Jun 2020 09:56:13: 16000000 INFO @ Tue, 16 Jun 2020 09:56:17: 13000000 INFO @ Tue, 16 Jun 2020 09:56:18: 22000000 INFO @ Tue, 16 Jun 2020 09:56:19: 17000000 INFO @ Tue, 16 Jun 2020 09:56:22: 14000000 INFO @ Tue, 16 Jun 2020 09:56:24: 23000000 INFO @ Tue, 16 Jun 2020 09:56:25: 18000000 INFO @ Tue, 16 Jun 2020 09:56:27: 15000000 INFO @ Tue, 16 Jun 2020 09:56:30: 24000000 INFO @ Tue, 16 Jun 2020 09:56:31: 19000000 INFO @ Tue, 16 Jun 2020 09:56:32: 16000000 INFO @ Tue, 16 Jun 2020 09:56:36: 25000000 INFO @ Tue, 16 Jun 2020 09:56:37: 20000000 INFO @ Tue, 16 Jun 2020 09:56:37: 17000000 INFO @ Tue, 16 Jun 2020 09:56:41: 26000000 INFO @ Tue, 16 Jun 2020 09:56:42: 18000000 INFO @ Tue, 16 Jun 2020 09:56:42: 21000000 INFO @ Tue, 16 Jun 2020 09:56:47: 19000000 INFO @ Tue, 16 Jun 2020 09:56:47: 27000000 INFO @ Tue, 16 Jun 2020 09:56:48: 22000000 INFO @ Tue, 16 Jun 2020 09:56:49: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:56:49: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:56:49: #1 total tags in treatment: 27343754 INFO @ Tue, 16 Jun 2020 09:56:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:56:49: #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 09:56:50: #1 tags after filtering in treatment: 27343754 INFO @ Tue, 16 Jun 2020 09:56:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:56:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:56:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:56:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:56:51: #2 number of paired peaks: 101 WARNING @ Tue, 16 Jun 2020 09:56:51: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Tue, 16 Jun 2020 09:56:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:56:52: start X-correlation... INFO @ Tue, 16 Jun 2020 09:56:52: end of X-cor INFO @ Tue, 16 Jun 2020 09:56:52: #2 finished! INFO @ Tue, 16 Jun 2020 09:56:52: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:56:52: #2 alternative fragment length(s) may be 1,41,590 bps INFO @ Tue, 16 Jun 2020 09:56:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.05_model.r WARNING @ Tue, 16 Jun 2020 09:56:52: #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 09:56:52: #2 You may need to consider one of the other alternative d(s): 1,41,590 WARNING @ Tue, 16 Jun 2020 09:56:52: #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 09:56:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:56:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:56:52: 20000000 INFO @ Tue, 16 Jun 2020 09:56:54: 23000000 INFO @ Tue, 16 Jun 2020 09:56:57: 21000000 INFO @ Tue, 16 Jun 2020 09:57:00: 24000000 INFO @ Tue, 16 Jun 2020 09:57:02: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:57:06: 25000000 INFO @ Tue, 16 Jun 2020 09:57:07: 23000000 INFO @ Tue, 16 Jun 2020 09:57:11: 26000000 INFO @ Tue, 16 Jun 2020 09:57:12: 24000000 INFO @ Tue, 16 Jun 2020 09:57:17: 25000000 INFO @ Tue, 16 Jun 2020 09:57:17: 27000000 INFO @ Tue, 16 Jun 2020 09:57:19: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:57:19: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:57:19: #1 total tags in treatment: 27343754 INFO @ Tue, 16 Jun 2020 09:57:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:57:19: #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 09:57:20: #1 tags after filtering in treatment: 27343754 INFO @ Tue, 16 Jun 2020 09:57:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:57:20: #1 finished! INFO @ Tue, 16 Jun 2020 09:57:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:57:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:57:21: #2 number of paired peaks: 101 WARNING @ Tue, 16 Jun 2020 09:57:21: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Tue, 16 Jun 2020 09:57:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:57:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:57:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:57:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:57:21: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:57:21: #2 alternative fragment length(s) may be 1,41,590 bps INFO @ Tue, 16 Jun 2020 09:57:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.10_model.r WARNING @ Tue, 16 Jun 2020 09:57:21: #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 09:57:21: #2 You may need to consider one of the other alternative d(s): 1,41,590 WARNING @ Tue, 16 Jun 2020 09:57:21: #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 09:57:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:57:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:57:22: 26000000 INFO @ Tue, 16 Jun 2020 09:57:27: 27000000 INFO @ Tue, 16 Jun 2020 09:57:28: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:57:28: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:57:28: #1 total tags in treatment: 27343754 INFO @ Tue, 16 Jun 2020 09:57:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:57:28: #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 09:57:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:57:29: #1 tags after filtering in treatment: 27343754 INFO @ Tue, 16 Jun 2020 09:57:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:57:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:57:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:57:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:57:30: #2 number of paired peaks: 101 WARNING @ Tue, 16 Jun 2020 09:57:30: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Tue, 16 Jun 2020 09:57:30: start model_add_line... INFO @ Tue, 16 Jun 2020 09:57:31: start X-correlation... INFO @ Tue, 16 Jun 2020 09:57:31: end of X-cor INFO @ Tue, 16 Jun 2020 09:57:31: #2 finished! INFO @ Tue, 16 Jun 2020 09:57:31: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:57:31: #2 alternative fragment length(s) may be 1,41,590 bps INFO @ Tue, 16 Jun 2020 09:57:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.20_model.r WARNING @ Tue, 16 Jun 2020 09:57:31: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:57:31: #2 You may need to consider one of the other alternative d(s): 1,41,590 WARNING @ Tue, 16 Jun 2020 09:57:31: #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 09:57:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:57:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:57:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:57:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:57:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.05_summits.bed INFO @ Tue, 16 Jun 2020 09:57:46: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:57:59: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:58:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:58:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:58:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:58:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.10_summits.bed INFO @ Tue, 16 Jun 2020 09:58:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:58:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:58:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:58:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619575/SRX6619575.20_summits.bed INFO @ Tue, 16 Jun 2020 09:58:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling