Job ID = 6367902 SRX = SRX4194194 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:46:29 prefetch.2.10.7: 1) Downloading 'SRR7291466'... 2020-06-15T23:46:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:48 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:48 prefetch.2.10.7: 'SRR7291466' is valid 2020-06-15T23:47:48 prefetch.2.10.7: 1) 'SRR7291466' was downloaded successfully 2020-06-15T23:47:48 prefetch.2.10.7: 'SRR7291466' has 0 unresolved dependencies Read 6289513 spots for SRR7291466/SRR7291466.sra Written 6289513 spots for SRR7291466/SRR7291466.sra 2020-06-15T23:48:25 prefetch.2.10.7: 1) Downloading 'SRR7291467'... 2020-06-15T23:48:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:25 prefetch.2.10.7: 'SRR7291467' is valid 2020-06-15T23:49:25 prefetch.2.10.7: 1) 'SRR7291467' was downloaded successfully 2020-06-15T23:49:25 prefetch.2.10.7: 'SRR7291467' has 0 unresolved dependencies Read 6164909 spots for SRR7291467/SRR7291467.sra Written 6164909 spots for SRR7291467/SRR7291467.sra 2020-06-15T23:50:00 prefetch.2.10.7: 1) Downloading 'SRR7291468'... 2020-06-15T23:50:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:25 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:25 prefetch.2.10.7: 'SRR7291468' is valid 2020-06-15T23:51:25 prefetch.2.10.7: 1) 'SRR7291468' was downloaded successfully 2020-06-15T23:51:25 prefetch.2.10.7: 'SRR7291468' has 0 unresolved dependencies Read 6287384 spots for SRR7291468/SRR7291468.sra Written 6287384 spots for SRR7291468/SRR7291468.sra 2020-06-15T23:51:58 prefetch.2.10.7: 1) Downloading 'SRR7291469'... 2020-06-15T23:51:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:53:19 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:53:19 prefetch.2.10.7: 'SRR7291469' is valid 2020-06-15T23:53:19 prefetch.2.10.7: 1) 'SRR7291469' was downloaded successfully 2020-06-15T23:53:19 prefetch.2.10.7: 'SRR7291469' has 0 unresolved dependencies Read 6101238 spots for SRR7291469/SRR7291469.sra Written 6101238 spots for SRR7291469/SRR7291469.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: 00:09:29 24843044 reads; of these: 24843044 (100.00%) were unpaired; of these: 1312183 (5.28%) aligned 0 times 18979192 (76.40%) aligned exactly 1 time 4551669 (18.32%) aligned >1 times 94.72% overall alignment rate Time searching: 00:09:29 Overall time: 00:09:29 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] 7718886 / 23530861 = 0.3280 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 09:10:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.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 09:10:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:33: 1000000 INFO @ Tue, 16 Jun 2020 09:10:39: 2000000 INFO @ Tue, 16 Jun 2020 09:10:45: 3000000 INFO @ Tue, 16 Jun 2020 09:10:50: 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 @ Tue, 16 Jun 2020 09:10:56: 5000000 INFO @ Tue, 16 Jun 2020 09:10:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.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 09:10:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:02: 6000000 INFO @ Tue, 16 Jun 2020 09:11:03: 1000000 INFO @ Tue, 16 Jun 2020 09:11:08: 7000000 INFO @ Tue, 16 Jun 2020 09:11:10: 2000000 INFO @ Tue, 16 Jun 2020 09:11:15: 8000000 INFO @ Tue, 16 Jun 2020 09:11:16: 3000000 INFO @ Tue, 16 Jun 2020 09:11:21: 9000000 INFO @ Tue, 16 Jun 2020 09:11:22: 4000000 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 09:11:27: 10000000 INFO @ Tue, 16 Jun 2020 09:11:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.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 09:11:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:29: 5000000 INFO @ Tue, 16 Jun 2020 09:11:33: 11000000 INFO @ Tue, 16 Jun 2020 09:11:34: 1000000 INFO @ Tue, 16 Jun 2020 09:11:35: 6000000 INFO @ Tue, 16 Jun 2020 09:11:39: 12000000 INFO @ Tue, 16 Jun 2020 09:11:40: 2000000 INFO @ Tue, 16 Jun 2020 09:11:41: 7000000 INFO @ Tue, 16 Jun 2020 09:11:46: 13000000 INFO @ Tue, 16 Jun 2020 09:11:47: 3000000 INFO @ Tue, 16 Jun 2020 09:11:48: 8000000 INFO @ Tue, 16 Jun 2020 09:11:52: 14000000 INFO @ Tue, 16 Jun 2020 09:11:53: 4000000 INFO @ Tue, 16 Jun 2020 09:11:54: 9000000 INFO @ Tue, 16 Jun 2020 09:11:58: 15000000 INFO @ Tue, 16 Jun 2020 09:11:59: 5000000 INFO @ Tue, 16 Jun 2020 09:12:00: 10000000 INFO @ Tue, 16 Jun 2020 09:12:03: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 09:12:03: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 09:12:03: #1 total tags in treatment: 15811975 INFO @ Tue, 16 Jun 2020 09:12:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:03: #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 09:12:03: #1 tags after filtering in treatment: 15811975 INFO @ Tue, 16 Jun 2020 09:12:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:04: #2 number of paired peaks: 387 WARNING @ Tue, 16 Jun 2020 09:12:04: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:05: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:05: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 09:12:05: #2 alternative fragment length(s) may be 2,44,58,560 bps INFO @ Tue, 16 Jun 2020 09:12:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.05_model.r WARNING @ Tue, 16 Jun 2020 09:12:05: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:05: #2 You may need to consider one of the other alternative d(s): 2,44,58,560 WARNING @ Tue, 16 Jun 2020 09:12:05: #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 09:12:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:06: 6000000 INFO @ Tue, 16 Jun 2020 09:12:06: 11000000 INFO @ Tue, 16 Jun 2020 09:12:12: 7000000 INFO @ Tue, 16 Jun 2020 09:12:12: 12000000 INFO @ Tue, 16 Jun 2020 09:12:18: 8000000 INFO @ Tue, 16 Jun 2020 09:12:18: 13000000 INFO @ Tue, 16 Jun 2020 09:12:24: 9000000 INFO @ Tue, 16 Jun 2020 09:12:24: 14000000 INFO @ Tue, 16 Jun 2020 09:12:30: 10000000 INFO @ Tue, 16 Jun 2020 09:12:31: 15000000 INFO @ Tue, 16 Jun 2020 09:12:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:36: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 09:12:36: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 09:12:36: #1 total tags in treatment: 15811975 INFO @ Tue, 16 Jun 2020 09:12:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:36: #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 09:12:36: 11000000 INFO @ Tue, 16 Jun 2020 09:12:36: #1 tags after filtering in treatment: 15811975 INFO @ Tue, 16 Jun 2020 09:12:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:36: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:37: #2 number of paired peaks: 387 WARNING @ Tue, 16 Jun 2020 09:12:37: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:37: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:37: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:37: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:37: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:37: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 09:12:37: #2 alternative fragment length(s) may be 2,44,58,560 bps INFO @ Tue, 16 Jun 2020 09:12:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.10_model.r WARNING @ Tue, 16 Jun 2020 09:12:37: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:37: #2 You may need to consider one of the other alternative d(s): 2,44,58,560 WARNING @ Tue, 16 Jun 2020 09:12:37: #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 09:12:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:42: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:12:47: 13000000 INFO @ Tue, 16 Jun 2020 09:12:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.05_summits.bed INFO @ Tue, 16 Jun 2020 09:12:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (667 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:53: 14000000 INFO @ Tue, 16 Jun 2020 09:12:59: 15000000 INFO @ Tue, 16 Jun 2020 09:13:04: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 09:13:04: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 09:13:04: #1 total tags in treatment: 15811975 INFO @ Tue, 16 Jun 2020 09:13:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:04: #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 09:13:04: #1 tags after filtering in treatment: 15811975 INFO @ Tue, 16 Jun 2020 09:13:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:13:04: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:05: #2 number of paired peaks: 387 WARNING @ Tue, 16 Jun 2020 09:13:05: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Tue, 16 Jun 2020 09:13:05: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:05: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:05: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 09:13:05: #2 alternative fragment length(s) may be 2,44,58,560 bps INFO @ Tue, 16 Jun 2020 09:13:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.20_model.r WARNING @ Tue, 16 Jun 2020 09:13:05: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:13:05: #2 You may need to consider one of the other alternative d(s): 2,44,58,560 WARNING @ Tue, 16 Jun 2020 09:13:05: #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 09:13:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.10_summits.bed INFO @ Tue, 16 Jun 2020 09:13:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (415 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:13:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194194/SRX4194194.20_summits.bed INFO @ Tue, 16 Jun 2020 09:13:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (163 records, 4 fields): 1 millis CompletedMACS2peakCalling