Job ID = 6366122 SRX = SRX065638 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:01:38 prefetch.2.10.7: 1) Downloading 'SRR217344'... 2020-06-15T23:01:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:02:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:02:00 prefetch.2.10.7: 'SRR217344' is valid 2020-06-15T23:02:00 prefetch.2.10.7: 1) 'SRR217344' was downloaded successfully Read 7060780 spots for SRR217344/SRR217344.sra Written 7060780 spots for SRR217344/SRR217344.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: 00:01:05 7060780 reads; of these: 7060780 (100.00%) were unpaired; of these: 157448 (2.23%) aligned 0 times 5878288 (83.25%) aligned exactly 1 time 1025044 (14.52%) aligned >1 times 97.77% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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] 1040443 / 6903332 = 0.1507 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 08:05:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.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 08:05:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:28: 1000000 INFO @ Tue, 16 Jun 2020 08:05:33: 2000000 INFO @ Tue, 16 Jun 2020 08:05:38: 3000000 INFO @ Tue, 16 Jun 2020 08:05:44: 4000000 INFO @ Tue, 16 Jun 2020 08:05:49: 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 08:05:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.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 08:05:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:53: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:05:53: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:05:53: #1 total tags in treatment: 5862889 INFO @ Tue, 16 Jun 2020 08:05:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:53: #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 08:05:53: #1 tags after filtering in treatment: 5862889 INFO @ Tue, 16 Jun 2020 08:05:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:05:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:05:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:05:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:05:54: #2 number of paired peaks: 241 WARNING @ Tue, 16 Jun 2020 08:05:54: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Tue, 16 Jun 2020 08:05:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:05:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:05:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:05:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:05:54: #2 predicted fragment length is 55 bps INFO @ Tue, 16 Jun 2020 08:05:54: #2 alternative fragment length(s) may be 3,55,580 bps INFO @ Tue, 16 Jun 2020 08:05:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.05_model.r WARNING @ Tue, 16 Jun 2020 08:05:54: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:05:54: #2 You may need to consider one of the other alternative d(s): 3,55,580 WARNING @ Tue, 16 Jun 2020 08:05:54: #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 08:05:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:05:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:05:59: 1000000 INFO @ Tue, 16 Jun 2020 08:06:05: 2000000 INFO @ Tue, 16 Jun 2020 08:06:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:11: 3000000 INFO @ Tue, 16 Jun 2020 08:06:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.05_summits.bed INFO @ Tue, 16 Jun 2020 08:06:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (317 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:06:16: 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 08:06:22: 5000000 INFO @ Tue, 16 Jun 2020 08:06:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.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 08:06:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:27: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:06:27: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:06:27: #1 total tags in treatment: 5862889 INFO @ Tue, 16 Jun 2020 08:06:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:27: #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 08:06:27: #1 tags after filtering in treatment: 5862889 INFO @ Tue, 16 Jun 2020 08:06:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:28: #2 number of paired peaks: 241 WARNING @ Tue, 16 Jun 2020 08:06:28: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:28: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:28: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:28: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:28: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:28: #2 predicted fragment length is 55 bps INFO @ Tue, 16 Jun 2020 08:06:28: #2 alternative fragment length(s) may be 3,55,580 bps INFO @ Tue, 16 Jun 2020 08:06:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.10_model.r WARNING @ Tue, 16 Jun 2020 08:06:28: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:28: #2 You may need to consider one of the other alternative d(s): 3,55,580 WARNING @ Tue, 16 Jun 2020 08:06:28: #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 08:06:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:29: 1000000 INFO @ Tue, 16 Jun 2020 08:06:35: 2000000 INFO @ Tue, 16 Jun 2020 08:06:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:41: 3000000 INFO @ Tue, 16 Jun 2020 08:06:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.10_summits.bed INFO @ Tue, 16 Jun 2020 08:06:45: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (136 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:06:47: 4000000 INFO @ Tue, 16 Jun 2020 08:06:53: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:06:58: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:06:58: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:06:58: #1 total tags in treatment: 5862889 INFO @ Tue, 16 Jun 2020 08:06:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:58: #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 08:06:58: #1 tags after filtering in treatment: 5862889 INFO @ Tue, 16 Jun 2020 08:06:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:59: #2 number of paired peaks: 241 WARNING @ Tue, 16 Jun 2020 08:06:59: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:59: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:59: #2 predicted fragment length is 55 bps INFO @ Tue, 16 Jun 2020 08:06:59: #2 alternative fragment length(s) may be 3,55,580 bps INFO @ Tue, 16 Jun 2020 08:06:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.20_model.r WARNING @ Tue, 16 Jun 2020 08:06:59: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:59: #2 You may need to consider one of the other alternative d(s): 3,55,580 WARNING @ Tue, 16 Jun 2020 08:06:59: #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 08:06:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:10: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:07:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065638/SRX065638.20_summits.bed INFO @ Tue, 16 Jun 2020 08:07:17: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (49 records, 4 fields): 1 millis CompletedMACS2peakCalling