Job ID = 6368235 SRX = SRX494918 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:01:15 prefetch.2.10.7: 1) Downloading 'SRR1198450'... 2020-06-16T00:01:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:02:43 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:02:43 prefetch.2.10.7: 1) 'SRR1198450' was downloaded successfully Read 15695316 spots for SRR1198450/SRR1198450.sra Written 15695316 spots for SRR1198450/SRR1198450.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: 00:03:19 15695316 reads; of these: 15695316 (100.00%) were unpaired; of these: 1826684 (11.64%) aligned 0 times 11335236 (72.22%) aligned exactly 1 time 2533396 (16.14%) aligned >1 times 88.36% overall alignment rate Time searching: 00:03:19 Overall time: 00:03:19 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 8 files... [bam_rmdupse_core] 1282055 / 13868632 = 0.0924 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 09:10:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.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 09:10:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:46: 1000000 INFO @ Tue, 16 Jun 2020 09:10:52: 2000000 INFO @ Tue, 16 Jun 2020 09:10:57: 3000000 INFO @ Tue, 16 Jun 2020 09:11:03: 4000000 INFO @ Tue, 16 Jun 2020 09:11:08: 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 09:11:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.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 09:11:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:14: 6000000 INFO @ Tue, 16 Jun 2020 09:11:17: 1000000 INFO @ Tue, 16 Jun 2020 09:11:21: 7000000 INFO @ Tue, 16 Jun 2020 09:11:23: 2000000 INFO @ Tue, 16 Jun 2020 09:11:27: 8000000 INFO @ Tue, 16 Jun 2020 09:11:30: 3000000 INFO @ Tue, 16 Jun 2020 09:11:33: 9000000 INFO @ Tue, 16 Jun 2020 09:11:36: 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 09:11:39: 10000000 INFO @ Tue, 16 Jun 2020 09:11:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.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 09:11:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:42: 5000000 INFO @ Tue, 16 Jun 2020 09:11:46: 11000000 INFO @ Tue, 16 Jun 2020 09:11:47: 1000000 INFO @ Tue, 16 Jun 2020 09:11:48: 6000000 INFO @ Tue, 16 Jun 2020 09:11:52: 12000000 INFO @ Tue, 16 Jun 2020 09:11:54: 2000000 INFO @ Tue, 16 Jun 2020 09:11:55: 7000000 INFO @ Tue, 16 Jun 2020 09:11:56: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:11:56: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:11:56: #1 total tags in treatment: 12586577 INFO @ Tue, 16 Jun 2020 09:11:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:56: #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 09:11:56: #1 tags after filtering in treatment: 12586577 INFO @ Tue, 16 Jun 2020 09:11:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:56: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:57: #2 number of paired peaks: 354 WARNING @ Tue, 16 Jun 2020 09:11:57: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:57: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:57: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:11:57: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 16 Jun 2020 09:11:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.05_model.r WARNING @ Tue, 16 Jun 2020 09:11:57: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:57: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 16 Jun 2020 09:11:57: #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 09:11:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:00: 3000000 INFO @ Tue, 16 Jun 2020 09:12:01: 8000000 INFO @ Tue, 16 Jun 2020 09:12:06: 4000000 INFO @ Tue, 16 Jun 2020 09:12:08: 9000000 INFO @ Tue, 16 Jun 2020 09:12:13: 5000000 INFO @ Tue, 16 Jun 2020 09:12:14: 10000000 INFO @ Tue, 16 Jun 2020 09:12:19: 6000000 INFO @ Tue, 16 Jun 2020 09:12:20: 11000000 INFO @ Tue, 16 Jun 2020 09:12:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:25: 7000000 INFO @ Tue, 16 Jun 2020 09:12:27: 12000000 INFO @ Tue, 16 Jun 2020 09:12:30: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:12:30: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:12:30: #1 total tags in treatment: 12586577 INFO @ Tue, 16 Jun 2020 09:12:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:30: #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 09:12:31: #1 tags after filtering in treatment: 12586577 INFO @ Tue, 16 Jun 2020 09:12:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:31: #2 number of paired peaks: 354 WARNING @ Tue, 16 Jun 2020 09:12:31: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:32: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:12:32: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 16 Jun 2020 09:12:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.10_model.r WARNING @ Tue, 16 Jun 2020 09:12:32: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:32: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 16 Jun 2020 09:12:32: #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 09:12:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:32: 8000000 INFO @ Tue, 16 Jun 2020 09:12:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.05_summits.bed INFO @ Tue, 16 Jun 2020 09:12:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (664 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:38: 9000000 INFO @ Tue, 16 Jun 2020 09:12:43: 10000000 INFO @ Tue, 16 Jun 2020 09:12:49: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:12:55: 12000000 INFO @ Tue, 16 Jun 2020 09:12:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:58: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:12:58: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:12:58: #1 total tags in treatment: 12586577 INFO @ Tue, 16 Jun 2020 09:12:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:58: #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 09:12:59: #1 tags after filtering in treatment: 12586577 INFO @ Tue, 16 Jun 2020 09:12:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:59: #2 number of paired peaks: 354 WARNING @ Tue, 16 Jun 2020 09:12:59: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:00: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:13:00: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 16 Jun 2020 09:13:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.20_model.r WARNING @ Tue, 16 Jun 2020 09:13:00: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:13:00: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 16 Jun 2020 09:13:00: #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 09:13:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.10_summits.bed INFO @ Tue, 16 Jun 2020 09:13:07: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (497 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:13:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494918/SRX494918.20_summits.bed INFO @ Tue, 16 Jun 2020 09:13:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (204 records, 4 fields): 1 millis CompletedMACS2peakCalling