Job ID = 8070390 SRX = SRX7217781 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 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: 00:14:42 8618829 reads; of these: 8618829 (100.00%) were paired; of these: 1958123 (22.72%) aligned concordantly 0 times 5757413 (66.80%) aligned concordantly exactly 1 time 903293 (10.48%) aligned concordantly >1 times ---- 1958123 pairs aligned concordantly 0 times; of these: 364214 (18.60%) aligned discordantly 1 time ---- 1593909 pairs aligned 0 times concordantly or discordantly; of these: 3187818 mates make up the pairs; of these: 2960433 (92.87%) aligned 0 times 142216 (4.46%) aligned exactly 1 time 85169 (2.67%) aligned >1 times 82.83% overall alignment rate Time searching: 00:14:42 Overall time: 00:14:42 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_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] 1142971 / 6992060 = 0.1635 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 13:24:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.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 13:24:28: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:24:28: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:24:37: 1000000 INFO @ Sat, 08 Aug 2020 13:24:46: 2000000 INFO @ Sat, 08 Aug 2020 13:24:54: 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 @ Sat, 08 Aug 2020 13:24:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.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 13:24:58: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:24:58: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:25:03: 4000000 INFO @ Sat, 08 Aug 2020 13:25:07: 1000000 INFO @ Sat, 08 Aug 2020 13:25:13: 5000000 INFO @ Sat, 08 Aug 2020 13:25:17: 2000000 INFO @ Sat, 08 Aug 2020 13:25:22: 6000000 INFO @ Sat, 08 Aug 2020 13:25:26: 3000000 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 @ Sat, 08 Aug 2020 13:25:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.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 13:25:28: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:25:28: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:25:31: 7000000 INFO @ Sat, 08 Aug 2020 13:25:36: 4000000 INFO @ Sat, 08 Aug 2020 13:25:36: 1000000 INFO @ Sat, 08 Aug 2020 13:25:41: 8000000 INFO @ Sat, 08 Aug 2020 13:25:44: 2000000 INFO @ Sat, 08 Aug 2020 13:25:45: 5000000 INFO @ Sat, 08 Aug 2020 13:25:50: 9000000 INFO @ Sat, 08 Aug 2020 13:25:52: 3000000 INFO @ Sat, 08 Aug 2020 13:25:55: 6000000 INFO @ Sat, 08 Aug 2020 13:26:00: 10000000 INFO @ Sat, 08 Aug 2020 13:26:00: 4000000 INFO @ Sat, 08 Aug 2020 13:26:04: 7000000 INFO @ Sat, 08 Aug 2020 13:26:08: 5000000 INFO @ Sat, 08 Aug 2020 13:26:09: 11000000 INFO @ Sat, 08 Aug 2020 13:26:14: 8000000 INFO @ Sat, 08 Aug 2020 13:26:16: 6000000 INFO @ Sat, 08 Aug 2020 13:26:19: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:26:19: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:26:19: #1 total tags in treatment: 5564171 INFO @ Sat, 08 Aug 2020 13:26:19: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:26:19: #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 13:26:19: #1 tags after filtering in treatment: 5122283 INFO @ Sat, 08 Aug 2020 13:26:19: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:26:19: #1 finished! INFO @ Sat, 08 Aug 2020 13:26:19: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:26:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:26:19: #2 number of paired peaks: 424 WARNING @ Sat, 08 Aug 2020 13:26:19: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Sat, 08 Aug 2020 13:26:19: start model_add_line... INFO @ Sat, 08 Aug 2020 13:26:19: start X-correlation... INFO @ Sat, 08 Aug 2020 13:26:19: end of X-cor INFO @ Sat, 08 Aug 2020 13:26:19: #2 finished! INFO @ Sat, 08 Aug 2020 13:26:19: #2 predicted fragment length is 215 bps INFO @ Sat, 08 Aug 2020 13:26:19: #2 alternative fragment length(s) may be 215 bps INFO @ Sat, 08 Aug 2020 13:26:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.05_model.r WARNING @ Sat, 08 Aug 2020 13:26:19: #2 Since the d (215) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:26:19: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Sat, 08 Aug 2020 13:26:19: #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 13:26:19: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:26:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:26:23: 9000000 INFO @ Sat, 08 Aug 2020 13:26:24: 7000000 INFO @ Sat, 08 Aug 2020 13:26:30: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:26:31: 8000000 INFO @ Sat, 08 Aug 2020 13:26:33: 10000000 INFO @ Sat, 08 Aug 2020 13:26:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:26:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:26:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.05_summits.bed INFO @ Sat, 08 Aug 2020 13:26:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (324 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:26:39: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:26:42: 11000000 INFO @ Sat, 08 Aug 2020 13:26:46: 10000000 INFO @ Sat, 08 Aug 2020 13:26:51: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:26:51: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:26:51: #1 total tags in treatment: 5564171 INFO @ Sat, 08 Aug 2020 13:26:51: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:26:51: #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 13:26:51: #1 tags after filtering in treatment: 5122283 INFO @ Sat, 08 Aug 2020 13:26:51: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:26:51: #1 finished! INFO @ Sat, 08 Aug 2020 13:26:51: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:26:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:26:52: #2 number of paired peaks: 424 WARNING @ Sat, 08 Aug 2020 13:26:52: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Sat, 08 Aug 2020 13:26:52: start model_add_line... INFO @ Sat, 08 Aug 2020 13:26:52: start X-correlation... INFO @ Sat, 08 Aug 2020 13:26:52: end of X-cor INFO @ Sat, 08 Aug 2020 13:26:52: #2 finished! INFO @ Sat, 08 Aug 2020 13:26:52: #2 predicted fragment length is 215 bps INFO @ Sat, 08 Aug 2020 13:26:52: #2 alternative fragment length(s) may be 215 bps INFO @ Sat, 08 Aug 2020 13:26:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.10_model.r WARNING @ Sat, 08 Aug 2020 13:26:52: #2 Since the d (215) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:26:52: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Sat, 08 Aug 2020 13:26:52: #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 13:26:52: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:26:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:26:54: 11000000 INFO @ Sat, 08 Aug 2020 13:27:01: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:27:01: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:27:01: #1 total tags in treatment: 5564171 INFO @ Sat, 08 Aug 2020 13:27:01: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:27:01: #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 13:27:01: #1 tags after filtering in treatment: 5122283 INFO @ Sat, 08 Aug 2020 13:27:01: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:27:01: #1 finished! INFO @ Sat, 08 Aug 2020 13:27:01: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:27:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:27:02: #2 number of paired peaks: 424 WARNING @ Sat, 08 Aug 2020 13:27:02: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Sat, 08 Aug 2020 13:27:02: start model_add_line... INFO @ Sat, 08 Aug 2020 13:27:02: start X-correlation... INFO @ Sat, 08 Aug 2020 13:27:02: end of X-cor INFO @ Sat, 08 Aug 2020 13:27:02: #2 finished! INFO @ Sat, 08 Aug 2020 13:27:02: #2 predicted fragment length is 215 bps INFO @ Sat, 08 Aug 2020 13:27:02: #2 alternative fragment length(s) may be 215 bps INFO @ Sat, 08 Aug 2020 13:27:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.20_model.r WARNING @ Sat, 08 Aug 2020 13:27:02: #2 Since the d (215) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:27:02: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Sat, 08 Aug 2020 13:27:02: #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 13:27:02: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:27:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:27:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:27:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:27:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:27:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.10_summits.bed INFO @ Sat, 08 Aug 2020 13:27:08: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (241 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:27:13: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:27:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:27:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:27:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217781/SRX7217781.20_summits.bed INFO @ Sat, 08 Aug 2020 13:27:18: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (178 records, 4 fields): 2 millis CompletedMACS2peakCalling