Job ID = 6497431 SRX = SRX494929 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:40:22 prefetch.2.10.7: 1) Downloading 'SRR1198461'... 2020-06-25T21:40:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:42:54 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:42:54 prefetch.2.10.7: 1) 'SRR1198461' was downloaded successfully Read 26129426 spots for SRR1198461/SRR1198461.sra Written 26129426 spots for SRR1198461/SRR1198461.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:05:34 26129426 reads; of these: 26129426 (100.00%) were unpaired; of these: 4253402 (16.28%) aligned 0 times 18035311 (69.02%) aligned exactly 1 time 3840713 (14.70%) aligned >1 times 83.72% overall alignment rate Time searching: 00:05:37 Overall time: 00:05:38 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 12 files... [bam_rmdupse_core] 15681105 / 21876024 = 0.7168 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 @ Fri, 26 Jun 2020 06:55:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.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 @ Fri, 26 Jun 2020 06:55:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:55:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:55:24: 1000000 INFO @ Fri, 26 Jun 2020 06:55:30: 2000000 INFO @ Fri, 26 Jun 2020 06:55:35: 3000000 INFO @ Fri, 26 Jun 2020 06:55:41: 4000000 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 @ Fri, 26 Jun 2020 06:55:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.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 @ Fri, 26 Jun 2020 06:55:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:55:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:55:47: 5000000 INFO @ Fri, 26 Jun 2020 06:55:53: 6000000 INFO @ Fri, 26 Jun 2020 06:55:54: 1000000 INFO @ Fri, 26 Jun 2020 06:55:54: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 06:55:54: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 06:55:54: #1 total tags in treatment: 6194919 INFO @ Fri, 26 Jun 2020 06:55:54: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:55:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 06:55:54: #1 tags after filtering in treatment: 6194919 INFO @ Fri, 26 Jun 2020 06:55:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:55:54: #1 finished! INFO @ Fri, 26 Jun 2020 06:55:54: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:55:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:55:55: #2 number of paired peaks: 729 WARNING @ Fri, 26 Jun 2020 06:55:55: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Fri, 26 Jun 2020 06:55:55: start model_add_line... INFO @ Fri, 26 Jun 2020 06:55:55: start X-correlation... INFO @ Fri, 26 Jun 2020 06:55:55: end of X-cor INFO @ Fri, 26 Jun 2020 06:55:55: #2 finished! INFO @ Fri, 26 Jun 2020 06:55:55: #2 predicted fragment length is 43 bps INFO @ Fri, 26 Jun 2020 06:55:55: #2 alternative fragment length(s) may be 3,43,569 bps INFO @ Fri, 26 Jun 2020 06:55:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.05_model.r WARNING @ Fri, 26 Jun 2020 06:55:55: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:55:55: #2 You may need to consider one of the other alternative d(s): 3,43,569 WARNING @ Fri, 26 Jun 2020 06:55:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 06:55:55: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:55:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:56:00: 2000000 INFO @ Fri, 26 Jun 2020 06:56:06: 3000000 INFO @ Fri, 26 Jun 2020 06:56:07: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:56:11: 4000000 INFO @ Fri, 26 Jun 2020 06:56:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.05_peaks.xls INFO @ Fri, 26 Jun 2020 06:56:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:56:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.05_summits.bed INFO @ Fri, 26 Jun 2020 06:56:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (868 records, 4 fields): 3 millis 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 CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:56:17: 5000000 INFO @ Fri, 26 Jun 2020 06:56:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.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 @ Fri, 26 Jun 2020 06:56:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:56:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:56:23: 6000000 INFO @ Fri, 26 Jun 2020 06:56:23: 1000000 INFO @ Fri, 26 Jun 2020 06:56:24: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 06:56:24: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 06:56:24: #1 total tags in treatment: 6194919 INFO @ Fri, 26 Jun 2020 06:56:24: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:56:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 06:56:24: #1 tags after filtering in treatment: 6194919 INFO @ Fri, 26 Jun 2020 06:56:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:56:24: #1 finished! INFO @ Fri, 26 Jun 2020 06:56:24: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:56:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:56:25: #2 number of paired peaks: 729 WARNING @ Fri, 26 Jun 2020 06:56:25: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Fri, 26 Jun 2020 06:56:25: start model_add_line... INFO @ Fri, 26 Jun 2020 06:56:25: start X-correlation... INFO @ Fri, 26 Jun 2020 06:56:25: end of X-cor INFO @ Fri, 26 Jun 2020 06:56:25: #2 finished! INFO @ Fri, 26 Jun 2020 06:56:25: #2 predicted fragment length is 43 bps INFO @ Fri, 26 Jun 2020 06:56:25: #2 alternative fragment length(s) may be 3,43,569 bps INFO @ Fri, 26 Jun 2020 06:56:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.10_model.r WARNING @ Fri, 26 Jun 2020 06:56:25: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:56:25: #2 You may need to consider one of the other alternative d(s): 3,43,569 WARNING @ Fri, 26 Jun 2020 06:56:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 06:56:25: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:56:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:56:29: 2000000 INFO @ Fri, 26 Jun 2020 06:56:35: 3000000 INFO @ Fri, 26 Jun 2020 06:56:37: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:56:40: 4000000 INFO @ Fri, 26 Jun 2020 06:56:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.10_peaks.xls INFO @ Fri, 26 Jun 2020 06:56:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:56:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.10_summits.bed INFO @ Fri, 26 Jun 2020 06:56:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (564 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:56:46: 5000000 INFO @ Fri, 26 Jun 2020 06:56:51: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 06:56:52: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 06:56:52: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 06:56:52: #1 total tags in treatment: 6194919 INFO @ Fri, 26 Jun 2020 06:56:52: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:56:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 06:56:53: #1 tags after filtering in treatment: 6194919 INFO @ Fri, 26 Jun 2020 06:56:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:56:53: #1 finished! INFO @ Fri, 26 Jun 2020 06:56:53: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:56:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:56:53: #2 number of paired peaks: 729 WARNING @ Fri, 26 Jun 2020 06:56:53: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Fri, 26 Jun 2020 06:56:53: start model_add_line... INFO @ Fri, 26 Jun 2020 06:56:53: start X-correlation... INFO @ Fri, 26 Jun 2020 06:56:53: end of X-cor INFO @ Fri, 26 Jun 2020 06:56:53: #2 finished! INFO @ Fri, 26 Jun 2020 06:56:53: #2 predicted fragment length is 43 bps INFO @ Fri, 26 Jun 2020 06:56:53: #2 alternative fragment length(s) may be 3,43,569 bps INFO @ Fri, 26 Jun 2020 06:56:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.20_model.r WARNING @ Fri, 26 Jun 2020 06:56:53: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:56:53: #2 You may need to consider one of the other alternative d(s): 3,43,569 WARNING @ Fri, 26 Jun 2020 06:56:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 06:56:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:56:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:57:05: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 06:57:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.20_peaks.xls INFO @ Fri, 26 Jun 2020 06:57:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:57:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494929/SRX494929.20_summits.bed INFO @ Fri, 26 Jun 2020 06:57:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (254 records, 4 fields): 2 millis CompletedMACS2peakCalling