Job ID = 6367484 SRX = SRX331241 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:31:35 prefetch.2.10.7: 1) Downloading 'SRR947473'... 2020-06-15T23:31:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:32:15 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:32:15 prefetch.2.10.7: 'SRR947473' is valid 2020-06-15T23:32:15 prefetch.2.10.7: 1) 'SRR947473' was downloaded successfully Read 7162487 spots for SRR947473/SRR947473.sra Written 7162487 spots for SRR947473/SRR947473.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: 00:01:07 7162487 reads; of these: 7162487 (100.00%) were unpaired; of these: 41305 (0.58%) aligned 0 times 6023996 (84.10%) aligned exactly 1 time 1097186 (15.32%) aligned >1 times 99.42% overall alignment rate Time searching: 00:01:07 Overall time: 00:01:07 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_rmdupse_core] 491926 / 7121182 = 0.0691 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 08:35:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.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 08:35:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:35: 1000000 INFO @ Tue, 16 Jun 2020 08:35:39: 2000000 INFO @ Tue, 16 Jun 2020 08:35:44: 3000000 INFO @ Tue, 16 Jun 2020 08:35:49: 4000000 INFO @ Tue, 16 Jun 2020 08:35:53: 5000000 INFO @ Tue, 16 Jun 2020 08:35:58: 6000000 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 08:36:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.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 08:36:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:00: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:36:00: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:36:00: #1 total tags in treatment: 6629256 INFO @ Tue, 16 Jun 2020 08:36:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:00: #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 08:36:01: #1 tags after filtering in treatment: 6629256 INFO @ Tue, 16 Jun 2020 08:36:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:01: #2 number of paired peaks: 316 WARNING @ Tue, 16 Jun 2020 08:36:01: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Tue, 16 Jun 2020 08:36:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:01: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 08:36:01: #2 alternative fragment length(s) may be 2,34,481,557 bps INFO @ Tue, 16 Jun 2020 08:36:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.05_model.r WARNING @ Tue, 16 Jun 2020 08:36:01: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:36:01: #2 You may need to consider one of the other alternative d(s): 2,34,481,557 WARNING @ Tue, 16 Jun 2020 08:36:01: #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 08:36:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:05: 1000000 INFO @ Tue, 16 Jun 2020 08:36:10: 2000000 INFO @ Tue, 16 Jun 2020 08:36:14: 3000000 INFO @ Tue, 16 Jun 2020 08:36:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:19: 4000000 INFO @ Tue, 16 Jun 2020 08:36:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.05_summits.bed INFO @ Tue, 16 Jun 2020 08:36:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (444 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:36:24: 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 08:36:29: 6000000 INFO @ Tue, 16 Jun 2020 08:36:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.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 08:36:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:32: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:36:32: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:36:32: #1 total tags in treatment: 6629256 INFO @ Tue, 16 Jun 2020 08:36:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:32: #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 08:36:32: #1 tags after filtering in treatment: 6629256 INFO @ Tue, 16 Jun 2020 08:36:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:33: #2 number of paired peaks: 316 WARNING @ Tue, 16 Jun 2020 08:36:33: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Tue, 16 Jun 2020 08:36:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:33: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 08:36:33: #2 alternative fragment length(s) may be 2,34,481,557 bps INFO @ Tue, 16 Jun 2020 08:36:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.10_model.r WARNING @ Tue, 16 Jun 2020 08:36:33: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:36:33: #2 You may need to consider one of the other alternative d(s): 2,34,481,557 WARNING @ Tue, 16 Jun 2020 08:36:33: #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 08:36:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:36: 1000000 INFO @ Tue, 16 Jun 2020 08:36:41: 2000000 INFO @ Tue, 16 Jun 2020 08:36:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:47: 3000000 INFO @ Tue, 16 Jun 2020 08:36:53: 4000000 INFO @ Tue, 16 Jun 2020 08:36:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.10_summits.bed INFO @ Tue, 16 Jun 2020 08:36:53: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (190 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:36:58: 5000000 INFO @ Tue, 16 Jun 2020 08:37:04: 6000000 INFO @ Tue, 16 Jun 2020 08:37:08: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:37:08: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:37:08: #1 total tags in treatment: 6629256 INFO @ Tue, 16 Jun 2020 08:37:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:08: #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 08:37:08: #1 tags after filtering in treatment: 6629256 INFO @ Tue, 16 Jun 2020 08:37:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:08: #2 number of paired peaks: 316 WARNING @ Tue, 16 Jun 2020 08:37:08: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Tue, 16 Jun 2020 08:37:08: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:08: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:08: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:08: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:08: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 08:37:08: #2 alternative fragment length(s) may be 2,34,481,557 bps INFO @ Tue, 16 Jun 2020 08:37:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.20_model.r WARNING @ Tue, 16 Jun 2020 08:37:08: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:37:08: #2 You may need to consider one of the other alternative d(s): 2,34,481,557 WARNING @ Tue, 16 Jun 2020 08:37:08: #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 08:37:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:37:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331241/SRX331241.20_summits.bed INFO @ Tue, 16 Jun 2020 08:37:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (54 records, 4 fields): 0 millis CompletedMACS2peakCalling