Job ID = 6367706 SRX = SRX395530 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:34:50 prefetch.2.10.7: 1) Downloading 'SRR1054260'... 2020-06-15T23:34:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:35:49 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:35:49 prefetch.2.10.7: 'SRR1054260' is valid 2020-06-15T23:35:49 prefetch.2.10.7: 1) 'SRR1054260' was downloaded successfully Read 3423069 spots for SRR1054260/SRR1054260.sra Written 3423069 spots for SRR1054260/SRR1054260.sra 2020-06-15T23:36:09 prefetch.2.10.7: 1) Downloading 'SRR1054261'... 2020-06-15T23:36:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:37:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:37:01 prefetch.2.10.7: 'SRR1054261' is valid 2020-06-15T23:37:01 prefetch.2.10.7: 1) 'SRR1054261' was downloaded successfully Read 4920932 spots for SRR1054261/SRR1054261.sra Written 4920932 spots for SRR1054261/SRR1054261.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: 00:00:01 Multiseed full-index search: 00:01:14 8344001 reads; of these: 8344001 (100.00%) were unpaired; of these: 43431 (0.52%) aligned 0 times 6945166 (83.24%) aligned exactly 1 time 1355404 (16.24%) aligned >1 times 99.48% overall alignment rate Time searching: 00:01:15 Overall time: 00:01:15 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] 873910 / 8300570 = 0.1053 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 08:40:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.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 08:40:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:32: 1000000 INFO @ Tue, 16 Jun 2020 08:40:36: 2000000 INFO @ Tue, 16 Jun 2020 08:40:40: 3000000 INFO @ Tue, 16 Jun 2020 08:40:45: 4000000 INFO @ Tue, 16 Jun 2020 08:40:49: 5000000 INFO @ Tue, 16 Jun 2020 08:40:53: 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 08:40:57: 7000000 INFO @ Tue, 16 Jun 2020 08:40:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.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 08:40:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:59: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:40:59: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:40:59: #1 total tags in treatment: 7426660 INFO @ Tue, 16 Jun 2020 08:40:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:59: #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 08:40:59: #1 tags after filtering in treatment: 7426660 INFO @ Tue, 16 Jun 2020 08:40:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:00: #2 number of paired peaks: 363 WARNING @ Tue, 16 Jun 2020 08:41:00: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Tue, 16 Jun 2020 08:41:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:00: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:41:00: #2 alternative fragment length(s) may be 2,30,530,577,598 bps INFO @ Tue, 16 Jun 2020 08:41:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.05_model.r WARNING @ Tue, 16 Jun 2020 08:41:00: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:41:00: #2 You may need to consider one of the other alternative d(s): 2,30,530,577,598 WARNING @ Tue, 16 Jun 2020 08:41:00: #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 08:41:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:41:03: 1000000 INFO @ Tue, 16 Jun 2020 08:41:08: 2000000 INFO @ Tue, 16 Jun 2020 08:41:13: 3000000 INFO @ Tue, 16 Jun 2020 08:41:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:18: 4000000 INFO @ Tue, 16 Jun 2020 08:41:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.05_summits.bed INFO @ Tue, 16 Jun 2020 08:41:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (502 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:41:23: 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 08:41:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.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 08:41:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:29: 6000000 INFO @ Tue, 16 Jun 2020 08:41:32: 1000000 INFO @ Tue, 16 Jun 2020 08:41:34: 7000000 INFO @ Tue, 16 Jun 2020 08:41:36: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:41:36: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:41:36: #1 total tags in treatment: 7426660 INFO @ Tue, 16 Jun 2020 08:41:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:36: #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 08:41:36: #1 tags after filtering in treatment: 7426660 INFO @ Tue, 16 Jun 2020 08:41:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:36: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:36: 2000000 INFO @ Tue, 16 Jun 2020 08:41:36: #2 number of paired peaks: 363 WARNING @ Tue, 16 Jun 2020 08:41:36: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Tue, 16 Jun 2020 08:41:36: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:37: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:37: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:37: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:37: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:41:37: #2 alternative fragment length(s) may be 2,30,530,577,598 bps INFO @ Tue, 16 Jun 2020 08:41:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.10_model.r WARNING @ Tue, 16 Jun 2020 08:41:37: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:41:37: #2 You may need to consider one of the other alternative d(s): 2,30,530,577,598 WARNING @ Tue, 16 Jun 2020 08:41:37: #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 08:41:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:41:41: 3000000 INFO @ Tue, 16 Jun 2020 08:41:45: 4000000 INFO @ Tue, 16 Jun 2020 08:41:50: 5000000 INFO @ Tue, 16 Jun 2020 08:41:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:54: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:41:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.10_summits.bed INFO @ Tue, 16 Jun 2020 08:41:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (239 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:41:58: 7000000 INFO @ Tue, 16 Jun 2020 08:42:00: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:42:00: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:42:00: #1 total tags in treatment: 7426660 INFO @ Tue, 16 Jun 2020 08:42:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:42:00: #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 08:42:00: #1 tags after filtering in treatment: 7426660 INFO @ Tue, 16 Jun 2020 08:42:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:42:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:42:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:42:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:42:01: #2 number of paired peaks: 363 WARNING @ Tue, 16 Jun 2020 08:42:01: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Tue, 16 Jun 2020 08:42:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:42:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:42:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:42:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:42:01: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:42:01: #2 alternative fragment length(s) may be 2,30,530,577,598 bps INFO @ Tue, 16 Jun 2020 08:42:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.20_model.r WARNING @ Tue, 16 Jun 2020 08:42:01: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:42:01: #2 You may need to consider one of the other alternative d(s): 2,30,530,577,598 WARNING @ Tue, 16 Jun 2020 08:42:01: #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 08:42:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:42:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:42:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:42:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395530/SRX395530.20_summits.bed INFO @ Tue, 16 Jun 2020 08:42:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (66 records, 4 fields): 1 millis CompletedMACS2peakCalling