Job ID = 6497488 SRX = SRX495009 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:00:40 prefetch.2.10.7: 1) Downloading 'SRR1198541'... 2020-06-25T22:00:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:01:36 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:01:37 prefetch.2.10.7: 'SRR1198541' is valid 2020-06-25T22:01:37 prefetch.2.10.7: 1) 'SRR1198541' was downloaded successfully Read 10075319 spots for SRR1198541/SRR1198541.sra Written 10075319 spots for SRR1198541/SRR1198541.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: 00:01:49 10075319 reads; of these: 10075319 (100.00%) were unpaired; of these: 1468387 (14.57%) aligned 0 times 6958998 (69.07%) aligned exactly 1 time 1647934 (16.36%) aligned >1 times 85.43% overall alignment rate Time searching: 00:01:49 Overall time: 00:01:49 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] 1385013 / 8606932 = 0.1609 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 07:06:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.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 07:06:11: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:06:11: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:06:17: 1000000 INFO @ Fri, 26 Jun 2020 07:06:22: 2000000 INFO @ Fri, 26 Jun 2020 07:06:28: 3000000 INFO @ Fri, 26 Jun 2020 07:06:34: 4000000 INFO @ Fri, 26 Jun 2020 07:06:39: 5000000 INFO @ Fri, 26 Jun 2020 07:06:45: 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 @ Fri, 26 Jun 2020 07:06:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.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 07:06:50: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:06:50: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:06:51: 7000000 INFO @ Fri, 26 Jun 2020 07:06:52: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:06:52: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:06:52: #1 total tags in treatment: 7221919 INFO @ Fri, 26 Jun 2020 07:06:52: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:06:52: #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 07:06:52: #1 tags after filtering in treatment: 7221919 INFO @ Fri, 26 Jun 2020 07:06:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:06:52: #1 finished! INFO @ Fri, 26 Jun 2020 07:06:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:06:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:06:53: #2 number of paired peaks: 553 WARNING @ Fri, 26 Jun 2020 07:06:53: Fewer paired peaks (553) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 553 pairs to build model! INFO @ Fri, 26 Jun 2020 07:06:53: start model_add_line... INFO @ Fri, 26 Jun 2020 07:06:53: start X-correlation... INFO @ Fri, 26 Jun 2020 07:06:53: end of X-cor INFO @ Fri, 26 Jun 2020 07:06:53: #2 finished! INFO @ Fri, 26 Jun 2020 07:06:53: #2 predicted fragment length is 66 bps INFO @ Fri, 26 Jun 2020 07:06:53: #2 alternative fragment length(s) may be 4,66 bps INFO @ Fri, 26 Jun 2020 07:06:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.05_model.r WARNING @ Fri, 26 Jun 2020 07:06:53: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:06:53: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Fri, 26 Jun 2020 07:06:53: #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 07:06:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:06:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:06:56: 1000000 INFO @ Fri, 26 Jun 2020 07:07:02: 2000000 INFO @ Fri, 26 Jun 2020 07:07:08: 3000000 BedGraph に変換中... INFO @ Fri, 26 Jun 2020 07:07:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:07:13: 4000000 INFO @ Fri, 26 Jun 2020 07:07:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:07:19: 5000000 INFO @ Fri, 26 Jun 2020 07:07:25: 6000000 INFO @ Fri, 26 Jun 2020 07:07:31: 7000000 INFO @ Fri, 26 Jun 2020 07:07:32: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:07:32: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:07:32: #1 total tags in treatment: 7221919 INFO @ Fri, 26 Jun 2020 07:07:32: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:07:32: #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 07:07:32: #1 tags after filtering in treatment: 7221919 INFO @ Fri, 26 Jun 2020 07:07:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:07:32: #1 finished! INFO @ Fri, 26 Jun 2020 07:07:32: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:07:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:07:33: #2 number of paired peaks: 553 WARNING @ Fri, 26 Jun 2020 07:07:33: Fewer paired peaks (553) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 553 pairs to build model! INFO @ Fri, 26 Jun 2020 07:07:33: start model_add_line... INFO @ Fri, 26 Jun 2020 07:07:33: start X-correlation... INFO @ Fri, 26 Jun 2020 07:07:33: end of X-cor INFO @ Fri, 26 Jun 2020 07:07:33: #2 finished! INFO @ Fri, 26 Jun 2020 07:07:33: #2 predicted fragment length is 66 bps INFO @ Fri, 26 Jun 2020 07:07:33: #2 alternative fragment length(s) may be 4,66 bps INFO @ Fri, 26 Jun 2020 07:07:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.10_model.r WARNING @ Fri, 26 Jun 2020 07:07:49: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:07:49: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Fri, 26 Jun 2020 07:07:49: #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 07:07:49: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:07:49: #3 Pre-compute pvalue-qvalue table... 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 07:07:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:07:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.05_summits.bed INFO @ Fri, 26 Jun 2020 07:07:50: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1804 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:07:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.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 07:07:51: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:07:51: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:07:59: 1000000 INFO @ Fri, 26 Jun 2020 07:08:06: 2000000 INFO @ Fri, 26 Jun 2020 07:08:06: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:08:13: 3000000 INFO @ Fri, 26 Jun 2020 07:08:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:08:20: 4000000 INFO @ Fri, 26 Jun 2020 07:08:27: 5000000 BedGraph に変換しました。 INFO @ Fri, 26 Jun 2020 07:08:34: 6000000 INFO @ Fri, 26 Jun 2020 07:08:40: 7000000 INFO @ Fri, 26 Jun 2020 07:08:42: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:08:42: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:08:42: #1 total tags in treatment: 7221919 INFO @ Fri, 26 Jun 2020 07:08:42: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:08:42: #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 07:08:42: #1 tags after filtering in treatment: 7221919 INFO @ Fri, 26 Jun 2020 07:08:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:08:42: #1 finished! INFO @ Fri, 26 Jun 2020 07:08:42: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:08:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:08:42: #2 number of paired peaks: 553 WARNING @ Fri, 26 Jun 2020 07:08:42: Fewer paired peaks (553) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 553 pairs to build model! INFO @ Fri, 26 Jun 2020 07:08:42: start model_add_line... INFO @ Fri, 26 Jun 2020 07:08:42: start X-correlation... INFO @ Fri, 26 Jun 2020 07:08:42: end of X-cor INFO @ Fri, 26 Jun 2020 07:08:42: #2 finished! INFO @ Fri, 26 Jun 2020 07:08:42: #2 predicted fragment length is 66 bps INFO @ Fri, 26 Jun 2020 07:08:42: #2 alternative fragment length(s) may be 4,66 bps INFO @ Fri, 26 Jun 2020 07:08:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.20_model.r INFO @ Fri, 26 Jun 2020 07:08:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.10_peaks.narrowPeak WARNING @ Fri, 26 Jun 2020 07:08:59: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:08:59: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Fri, 26 Jun 2020 07:08:59: #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 07:08:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:08:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:08:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.10_summits.bed INFO @ Fri, 26 Jun 2020 07:08:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (626 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:09:17: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:09:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:09:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:09:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495009/SRX495009.20_summits.bed INFO @ Fri, 26 Jun 2020 07:09:35: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (221 records, 4 fields): 2 millis CompletedMACS2peakCalling