Job ID = 6368069 SRX = SRX466532 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:54:33 prefetch.2.10.7: 1) Downloading 'SRR1163598'... 2020-06-15T23:54:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:57:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:57:52 prefetch.2.10.7: 1) 'SRR1163598' was downloaded successfully Read 21509609 spots for SRR1163598/SRR1163598.sra Written 21509609 spots for SRR1163598/SRR1163598.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: 00:04:05 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 255394 (1.19%) aligned 0 times 17821508 (82.85%) aligned exactly 1 time 3432707 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:04:05 Overall time: 00:04:06 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] 3668231 / 21254215 = 0.1726 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 09:08:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.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 09:08:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:25: 1000000 INFO @ Tue, 16 Jun 2020 09:08:30: 2000000 INFO @ Tue, 16 Jun 2020 09:08:35: 3000000 INFO @ Tue, 16 Jun 2020 09:08:40: 4000000 INFO @ Tue, 16 Jun 2020 09:08:45: 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 09:08:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.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 09:08:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:50: 6000000 INFO @ Tue, 16 Jun 2020 09:08:55: 7000000 INFO @ Tue, 16 Jun 2020 09:08:56: 1000000 INFO @ Tue, 16 Jun 2020 09:09:01: 8000000 INFO @ Tue, 16 Jun 2020 09:09:01: 2000000 INFO @ Tue, 16 Jun 2020 09:09:06: 9000000 INFO @ Tue, 16 Jun 2020 09:09:07: 3000000 INFO @ Tue, 16 Jun 2020 09:09:11: 10000000 INFO @ Tue, 16 Jun 2020 09:09:12: 4000000 INFO @ Tue, 16 Jun 2020 09:09:16: 11000000 INFO @ Tue, 16 Jun 2020 09:09:18: 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 09:09:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.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 09:09:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:21: 12000000 INFO @ Tue, 16 Jun 2020 09:09:23: 6000000 INFO @ Tue, 16 Jun 2020 09:09:25: 1000000 INFO @ Tue, 16 Jun 2020 09:09:26: 13000000 INFO @ Tue, 16 Jun 2020 09:09:29: 7000000 INFO @ Tue, 16 Jun 2020 09:09:30: 2000000 INFO @ Tue, 16 Jun 2020 09:09:31: 14000000 INFO @ Tue, 16 Jun 2020 09:09:34: 8000000 INFO @ Tue, 16 Jun 2020 09:09:35: 3000000 INFO @ Tue, 16 Jun 2020 09:09:36: 15000000 INFO @ Tue, 16 Jun 2020 09:09:40: 9000000 INFO @ Tue, 16 Jun 2020 09:09:40: 4000000 INFO @ Tue, 16 Jun 2020 09:09:41: 16000000 INFO @ Tue, 16 Jun 2020 09:09:45: 10000000 INFO @ Tue, 16 Jun 2020 09:09:45: 5000000 INFO @ Tue, 16 Jun 2020 09:09:46: 17000000 INFO @ Tue, 16 Jun 2020 09:09:49: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:09:49: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:09:49: #1 total tags in treatment: 17585984 INFO @ Tue, 16 Jun 2020 09:09:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:09:49: #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 09:09:49: #1 tags after filtering in treatment: 17585984 INFO @ Tue, 16 Jun 2020 09:09:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:09:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:09:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:09:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:09:50: 6000000 INFO @ Tue, 16 Jun 2020 09:09:50: #2 number of paired peaks: 210 WARNING @ Tue, 16 Jun 2020 09:09:50: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Tue, 16 Jun 2020 09:09:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:09:50: 11000000 INFO @ Tue, 16 Jun 2020 09:09:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:09:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:09:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:09:51: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 09:09:51: #2 alternative fragment length(s) may be 1,39,552,575 bps INFO @ Tue, 16 Jun 2020 09:09:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.05_model.r WARNING @ Tue, 16 Jun 2020 09:09:51: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:09:51: #2 You may need to consider one of the other alternative d(s): 1,39,552,575 WARNING @ Tue, 16 Jun 2020 09:09:51: #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 09:09:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:09:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:09:55: 7000000 INFO @ Tue, 16 Jun 2020 09:09:56: 12000000 INFO @ Tue, 16 Jun 2020 09:10:00: 8000000 INFO @ Tue, 16 Jun 2020 09:10:01: 13000000 INFO @ Tue, 16 Jun 2020 09:10:05: 9000000 INFO @ Tue, 16 Jun 2020 09:10:06: 14000000 INFO @ Tue, 16 Jun 2020 09:10:11: 10000000 INFO @ Tue, 16 Jun 2020 09:10:12: 15000000 INFO @ Tue, 16 Jun 2020 09:10:16: 11000000 INFO @ Tue, 16 Jun 2020 09:10:17: 16000000 INFO @ Tue, 16 Jun 2020 09:10:21: 12000000 INFO @ Tue, 16 Jun 2020 09:10:22: 17000000 INFO @ Tue, 16 Jun 2020 09:10:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:26: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:10:26: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:10:26: #1 total tags in treatment: 17585984 INFO @ Tue, 16 Jun 2020 09:10:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:26: #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 09:10:26: 13000000 INFO @ Tue, 16 Jun 2020 09:10:26: #1 tags after filtering in treatment: 17585984 INFO @ Tue, 16 Jun 2020 09:10:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:27: #2 number of paired peaks: 210 WARNING @ Tue, 16 Jun 2020 09:10:27: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:27: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:27: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:27: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:27: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:27: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 09:10:27: #2 alternative fragment length(s) may be 1,39,552,575 bps INFO @ Tue, 16 Jun 2020 09:10:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.10_model.r WARNING @ Tue, 16 Jun 2020 09:10:27: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:10:27: #2 You may need to consider one of the other alternative d(s): 1,39,552,575 WARNING @ Tue, 16 Jun 2020 09:10:27: #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 09:10:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:31: 14000000 INFO @ Tue, 16 Jun 2020 09:10:36: 15000000 INFO @ Tue, 16 Jun 2020 09:10:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.05_summits.bed INFO @ Tue, 16 Jun 2020 09:10:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (697 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:10:41: 16000000 INFO @ Tue, 16 Jun 2020 09:10:46: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:10:49: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:10:49: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:10:49: #1 total tags in treatment: 17585984 INFO @ Tue, 16 Jun 2020 09:10:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:49: #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 09:10:49: #1 tags after filtering in treatment: 17585984 INFO @ Tue, 16 Jun 2020 09:10:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:51: #2 number of paired peaks: 210 WARNING @ Tue, 16 Jun 2020 09:10:51: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:51: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 09:10:51: #2 alternative fragment length(s) may be 1,39,552,575 bps INFO @ Tue, 16 Jun 2020 09:10:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.20_model.r WARNING @ Tue, 16 Jun 2020 09:10:51: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:10:51: #2 You may need to consider one of the other alternative d(s): 1,39,552,575 WARNING @ Tue, 16 Jun 2020 09:10:51: #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 09:10:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.10_summits.bed INFO @ Tue, 16 Jun 2020 09:11:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (327 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:11:23: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:11:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466532/SRX466532.20_summits.bed INFO @ Tue, 16 Jun 2020 09:11:40: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (104 records, 4 fields): 1 millis CompletedMACS2peakCalling