Job ID = 8069363 SRX = SRX7217779 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:31:38 prefetch.2.10.7: 1) Downloading 'SRR10533856'... 2020-08-08T03:31:38 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:34:23 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:34:23 prefetch.2.10.7: 1) 'SRR10533856' was downloaded successfully 2020-08-08T03:34:23 prefetch.2.10.7: 'SRR10533856' has 0 unresolved dependencies Read 7842201 spots for SRR10533856/SRR10533856.sra Written 7842201 spots for SRR10533856/SRR10533856.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070296 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:53 7842201 reads; of these: 7842201 (100.00%) were paired; of these: 3445799 (43.94%) aligned concordantly 0 times 3700949 (47.19%) aligned concordantly exactly 1 time 695453 (8.87%) aligned concordantly >1 times ---- 3445799 pairs aligned concordantly 0 times; of these: 707745 (20.54%) aligned discordantly 1 time ---- 2738054 pairs aligned 0 times concordantly or discordantly; of these: 5476108 mates make up the pairs; of these: 5133844 (93.75%) aligned 0 times 195533 (3.57%) aligned exactly 1 time 146731 (2.68%) aligned >1 times 67.27% overall alignment rate Time searching: 00:12:53 Overall time: 00:12:53 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 8 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 745830 / 5056326 = 0.1475 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 @ Sat, 08 Aug 2020 12:52:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.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 @ Sat, 08 Aug 2020 12:52:33: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:52:33: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:52:40: 1000000 INFO @ Sat, 08 Aug 2020 12:52:46: 2000000 INFO @ Sat, 08 Aug 2020 12:52:52: 3000000 INFO @ Sat, 08 Aug 2020 12:52:59: 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 @ Sat, 08 Aug 2020 12:53:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.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 @ Sat, 08 Aug 2020 12:53:03: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:53:03: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:53:05: 5000000 INFO @ Sat, 08 Aug 2020 12:53:09: 1000000 INFO @ Sat, 08 Aug 2020 12:53:11: 6000000 INFO @ Sat, 08 Aug 2020 12:53:15: 2000000 INFO @ Sat, 08 Aug 2020 12:53:17: 7000000 INFO @ Sat, 08 Aug 2020 12:53:22: 3000000 INFO @ Sat, 08 Aug 2020 12:53:24: 8000000 INFO @ Sat, 08 Aug 2020 12:53:29: 4000000 INFO @ Sat, 08 Aug 2020 12:53:30: 9000000 INFO @ Sat, 08 Aug 2020 12:53:31: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:53:31: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:53:31: #1 total tags in treatment: 3730289 INFO @ Sat, 08 Aug 2020 12:53:31: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:53:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:53:31: #1 tags after filtering in treatment: 3419842 INFO @ Sat, 08 Aug 2020 12:53:31: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 12:53:31: #1 finished! INFO @ Sat, 08 Aug 2020 12:53:31: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:53:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:53:31: #2 number of paired peaks: 493 WARNING @ Sat, 08 Aug 2020 12:53:31: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Sat, 08 Aug 2020 12:53:31: start model_add_line... INFO @ Sat, 08 Aug 2020 12:53:31: start X-correlation... INFO @ Sat, 08 Aug 2020 12:53:31: end of X-cor INFO @ Sat, 08 Aug 2020 12:53:31: #2 finished! INFO @ Sat, 08 Aug 2020 12:53:31: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 12:53:31: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 08 Aug 2020 12:53:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.05_model.r BedGraph に変換中... WARNING @ Sat, 08 Aug 2020 12:53:31: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:53:31: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Sat, 08 Aug 2020 12:53:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:53:31: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:53:31: #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 @ Sat, 08 Aug 2020 12:53:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.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 @ Sat, 08 Aug 2020 12:53:33: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:53:33: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:53:35: 5000000 INFO @ Sat, 08 Aug 2020 12:53:39: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:53:39: 1000000 INFO @ Sat, 08 Aug 2020 12:53:42: 6000000 INFO @ Sat, 08 Aug 2020 12:53:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:53:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:53:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.05_summits.bed INFO @ Sat, 08 Aug 2020 12:53:43: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (391 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:53:46: 2000000 INFO @ Sat, 08 Aug 2020 12:53:49: 7000000 INFO @ Sat, 08 Aug 2020 12:53:52: 3000000 INFO @ Sat, 08 Aug 2020 12:53:55: 8000000 INFO @ Sat, 08 Aug 2020 12:53:59: 4000000 INFO @ Sat, 08 Aug 2020 12:54:02: 9000000 INFO @ Sat, 08 Aug 2020 12:54:02: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:54:02: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:54:02: #1 total tags in treatment: 3730289 INFO @ Sat, 08 Aug 2020 12:54:02: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:54:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:54:02: #1 tags after filtering in treatment: 3419842 INFO @ Sat, 08 Aug 2020 12:54:02: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 12:54:02: #1 finished! INFO @ Sat, 08 Aug 2020 12:54:02: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:54:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:54:02: #2 number of paired peaks: 493 WARNING @ Sat, 08 Aug 2020 12:54:02: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Sat, 08 Aug 2020 12:54:02: start model_add_line... INFO @ Sat, 08 Aug 2020 12:54:02: start X-correlation... INFO @ Sat, 08 Aug 2020 12:54:02: end of X-cor INFO @ Sat, 08 Aug 2020 12:54:02: #2 finished! INFO @ Sat, 08 Aug 2020 12:54:02: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 12:54:02: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 08 Aug 2020 12:54:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.10_model.r WARNING @ Sat, 08 Aug 2020 12:54:02: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:54:02: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Sat, 08 Aug 2020 12:54:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:54:02: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:54:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:54:05: 5000000 INFO @ Sat, 08 Aug 2020 12:54:11: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:54:11: 6000000 INFO @ Sat, 08 Aug 2020 12:54:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:54:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:54:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.10_summits.bed INFO @ Sat, 08 Aug 2020 12:54:14: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (261 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:54:17: 7000000 INFO @ Sat, 08 Aug 2020 12:54:23: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:54:30: 9000000 INFO @ Sat, 08 Aug 2020 12:54:30: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:54:30: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:54:30: #1 total tags in treatment: 3730289 INFO @ Sat, 08 Aug 2020 12:54:30: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:54:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:54:30: #1 tags after filtering in treatment: 3419842 INFO @ Sat, 08 Aug 2020 12:54:30: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 12:54:30: #1 finished! INFO @ Sat, 08 Aug 2020 12:54:30: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:54:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:54:30: #2 number of paired peaks: 493 WARNING @ Sat, 08 Aug 2020 12:54:30: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Sat, 08 Aug 2020 12:54:30: start model_add_line... INFO @ Sat, 08 Aug 2020 12:54:30: start X-correlation... INFO @ Sat, 08 Aug 2020 12:54:30: end of X-cor INFO @ Sat, 08 Aug 2020 12:54:30: #2 finished! INFO @ Sat, 08 Aug 2020 12:54:30: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 12:54:30: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 08 Aug 2020 12:54:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.20_model.r WARNING @ Sat, 08 Aug 2020 12:54:30: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:54:30: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Sat, 08 Aug 2020 12:54:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:54:30: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:54:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:54:38: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:54:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:54:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:54:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217779/SRX7217779.20_summits.bed INFO @ Sat, 08 Aug 2020 12:54:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (174 records, 4 fields): 1 millis CompletedMACS2peakCalling