Job ID = 6366754 SRX = SRX2228907 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:54:59 prefetch.2.10.7: 1) Downloading 'SRR4380363'... 2020-06-15T22:54:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:56:07 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:56:07 prefetch.2.10.7: 'SRR4380363' is valid 2020-06-15T22:56:07 prefetch.2.10.7: 1) 'SRR4380363' was downloaded successfully 2020-06-15T22:56:07 prefetch.2.10.7: 'SRR4380363' has 0 unresolved dependencies Read 9276705 spots for SRR4380363/SRR4380363.sra Written 9276705 spots for SRR4380363/SRR4380363.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: 00:02:16 9276705 reads; of these: 9276705 (100.00%) were unpaired; of these: 85128 (0.92%) aligned 0 times 7666279 (82.64%) aligned exactly 1 time 1525298 (16.44%) aligned >1 times 99.08% overall alignment rate Time searching: 00:02:16 Overall time: 00:02:16 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] 1486014 / 9191577 = 0.1617 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 08:01:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.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 08:01:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:01:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:42: 1000000 INFO @ Tue, 16 Jun 2020 08:01:49: 2000000 INFO @ Tue, 16 Jun 2020 08:01:57: 3000000 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 08:02:04: 4000000 INFO @ Tue, 16 Jun 2020 08:02:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.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 08:02:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:11: 5000000 INFO @ Tue, 16 Jun 2020 08:02:12: 1000000 INFO @ Tue, 16 Jun 2020 08:02:19: 6000000 INFO @ Tue, 16 Jun 2020 08:02:20: 2000000 INFO @ Tue, 16 Jun 2020 08:02:27: 3000000 INFO @ Tue, 16 Jun 2020 08:02:27: 7000000 INFO @ Tue, 16 Jun 2020 08:02:33: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:02:33: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:02:33: #1 total tags in treatment: 7705563 INFO @ Tue, 16 Jun 2020 08:02:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:33: #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 08:02:33: #1 tags after filtering in treatment: 7705563 INFO @ Tue, 16 Jun 2020 08:02:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:33: #2 looking for paired plus/minus strand peaks... 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 08:02:33: #2 number of paired peaks: 355 WARNING @ Tue, 16 Jun 2020 08:02:33: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Tue, 16 Jun 2020 08:02:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:33: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 08:02:33: #2 alternative fragment length(s) may be 4,51,565 bps INFO @ Tue, 16 Jun 2020 08:02:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.05_model.r WARNING @ Tue, 16 Jun 2020 08:02:33: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:02:33: #2 You may need to consider one of the other alternative d(s): 4,51,565 WARNING @ Tue, 16 Jun 2020 08:02:33: #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 08:02:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:02:34: 4000000 INFO @ Tue, 16 Jun 2020 08:02:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.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 08:02:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:41: 5000000 INFO @ Tue, 16 Jun 2020 08:02:42: 1000000 INFO @ Tue, 16 Jun 2020 08:02:47: 6000000 INFO @ Tue, 16 Jun 2020 08:02:49: 2000000 INFO @ Tue, 16 Jun 2020 08:02:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:02:54: 7000000 INFO @ Tue, 16 Jun 2020 08:02:55: 3000000 INFO @ Tue, 16 Jun 2020 08:02:58: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:02:58: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:02:58: #1 total tags in treatment: 7705563 INFO @ Tue, 16 Jun 2020 08:02:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:58: #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 08:02:58: #1 tags after filtering in treatment: 7705563 INFO @ Tue, 16 Jun 2020 08:02:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:02:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:02:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:02:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.05_summits.bed INFO @ Tue, 16 Jun 2020 08:02:58: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (551 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:02:58: #2 number of paired peaks: 355 WARNING @ Tue, 16 Jun 2020 08:02:58: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Tue, 16 Jun 2020 08:02:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:59: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 08:02:59: #2 alternative fragment length(s) may be 4,51,565 bps INFO @ Tue, 16 Jun 2020 08:02:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.10_model.r WARNING @ Tue, 16 Jun 2020 08:02:59: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:02:59: #2 You may need to consider one of the other alternative d(s): 4,51,565 WARNING @ Tue, 16 Jun 2020 08:02:59: #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 08:02:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:03:01: 4000000 INFO @ Tue, 16 Jun 2020 08:03:07: 5000000 INFO @ Tue, 16 Jun 2020 08:03:13: 6000000 INFO @ Tue, 16 Jun 2020 08:03:14: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:03:20: 7000000 INFO @ Tue, 16 Jun 2020 08:03:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.10_summits.bed INFO @ Tue, 16 Jun 2020 08:03:22: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (335 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:03:24: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:03:24: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:03:24: #1 total tags in treatment: 7705563 INFO @ Tue, 16 Jun 2020 08:03:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:24: #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 08:03:24: #1 tags after filtering in treatment: 7705563 INFO @ Tue, 16 Jun 2020 08:03:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:24: #2 number of paired peaks: 355 WARNING @ Tue, 16 Jun 2020 08:03:24: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Tue, 16 Jun 2020 08:03:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:24: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 08:03:24: #2 alternative fragment length(s) may be 4,51,565 bps INFO @ Tue, 16 Jun 2020 08:03:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.20_model.r WARNING @ Tue, 16 Jun 2020 08:03:24: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:03:24: #2 You may need to consider one of the other alternative d(s): 4,51,565 WARNING @ Tue, 16 Jun 2020 08:03:24: #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 08:03:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:03:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:03:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228907/SRX2228907.20_summits.bed INFO @ Tue, 16 Jun 2020 08:03:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (154 records, 4 fields): 17 millis CompletedMACS2peakCalling