Job ID = 6366588 SRX = SRX2035135 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T22:58:23 prefetch.2.10.7: 1) Downloading 'SRR4044259'... 2020-06-15T22:58:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:00:40 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:00:40 prefetch.2.10.7: 1) 'SRR4044259' was downloaded successfully Read 7568721 spots for SRR4044259/SRR4044259.sra Written 7568721 spots for SRR4044259/SRR4044259.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: 00:10:44 7568721 reads; of these: 7568721 (100.00%) were paired; of these: 674799 (8.92%) aligned concordantly 0 times 5877839 (77.66%) aligned concordantly exactly 1 time 1016083 (13.42%) aligned concordantly >1 times ---- 674799 pairs aligned concordantly 0 times; of these: 422464 (62.61%) aligned discordantly 1 time ---- 252335 pairs aligned 0 times concordantly or discordantly; of these: 504670 mates make up the pairs; of these: 332155 (65.82%) aligned 0 times 70975 (14.06%) aligned exactly 1 time 101540 (20.12%) aligned >1 times 97.81% overall alignment rate Time searching: 00:10:44 Overall time: 00:10:44 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] 35223 / 7263989 = 0.0048 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 08:19:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.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 08:19:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:37: 1000000 INFO @ Tue, 16 Jun 2020 08:19:44: 2000000 INFO @ Tue, 16 Jun 2020 08:19:51: 3000000 INFO @ Tue, 16 Jun 2020 08:19:57: 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 @ Tue, 16 Jun 2020 08:20:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.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 08:20:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:04: 5000000 INFO @ Tue, 16 Jun 2020 08:20:08: 1000000 INFO @ Tue, 16 Jun 2020 08:20:12: 6000000 INFO @ Tue, 16 Jun 2020 08:20:15: 2000000 INFO @ Tue, 16 Jun 2020 08:20:19: 7000000 INFO @ Tue, 16 Jun 2020 08:20:23: 3000000 INFO @ Tue, 16 Jun 2020 08:20:27: 8000000 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 08:20:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.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 08:20:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:31: 4000000 INFO @ Tue, 16 Jun 2020 08:20:35: 9000000 INFO @ Tue, 16 Jun 2020 08:20:38: 1000000 INFO @ Tue, 16 Jun 2020 08:20:39: 5000000 INFO @ Tue, 16 Jun 2020 08:20:43: 10000000 INFO @ Tue, 16 Jun 2020 08:20:46: 2000000 INFO @ Tue, 16 Jun 2020 08:20:47: 6000000 INFO @ Tue, 16 Jun 2020 08:20:51: 11000000 INFO @ Tue, 16 Jun 2020 08:20:55: 3000000 INFO @ Tue, 16 Jun 2020 08:20:55: 7000000 INFO @ Tue, 16 Jun 2020 08:20:59: 12000000 INFO @ Tue, 16 Jun 2020 08:21:03: 4000000 INFO @ Tue, 16 Jun 2020 08:21:04: 8000000 INFO @ Tue, 16 Jun 2020 08:21:07: 13000000 INFO @ Tue, 16 Jun 2020 08:21:11: 5000000 INFO @ Tue, 16 Jun 2020 08:21:12: 9000000 INFO @ Tue, 16 Jun 2020 08:21:14: 14000000 INFO @ Tue, 16 Jun 2020 08:21:20: 6000000 INFO @ Tue, 16 Jun 2020 08:21:20: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:21:20: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:21:20: #1 total tags in treatment: 6859455 INFO @ Tue, 16 Jun 2020 08:21:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:20: #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 08:21:20: 10000000 INFO @ Tue, 16 Jun 2020 08:21:20: #1 tags after filtering in treatment: 6342605 INFO @ Tue, 16 Jun 2020 08:21:20: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 08:21:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:21: #2 number of paired peaks: 393 WARNING @ Tue, 16 Jun 2020 08:21:21: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Tue, 16 Jun 2020 08:21:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:21: #2 predicted fragment length is 179 bps INFO @ Tue, 16 Jun 2020 08:21:21: #2 alternative fragment length(s) may be 179 bps INFO @ Tue, 16 Jun 2020 08:21:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.05_model.r WARNING @ Tue, 16 Jun 2020 08:21:21: #2 Since the d (179) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:21:21: #2 You may need to consider one of the other alternative d(s): 179 WARNING @ Tue, 16 Jun 2020 08:21:21: #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 08:21:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:27: 7000000 INFO @ Tue, 16 Jun 2020 08:21:28: 11000000 INFO @ Tue, 16 Jun 2020 08:21:35: 8000000 INFO @ Tue, 16 Jun 2020 08:21:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:35: 12000000 INFO @ Tue, 16 Jun 2020 08:21:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:42: 9000000 INFO @ Tue, 16 Jun 2020 08:21:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.05_summits.bed INFO @ Tue, 16 Jun 2020 08:21:42: Done! INFO @ Tue, 16 Jun 2020 08:21:42: 13000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (665 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:21:49: 10000000 INFO @ Tue, 16 Jun 2020 08:21:50: 14000000 INFO @ Tue, 16 Jun 2020 08:21:55: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:21:55: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:21:55: #1 total tags in treatment: 6859455 INFO @ Tue, 16 Jun 2020 08:21:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:55: #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 08:21:55: #1 tags after filtering in treatment: 6342605 INFO @ Tue, 16 Jun 2020 08:21:55: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 08:21:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:56: #2 number of paired peaks: 393 WARNING @ Tue, 16 Jun 2020 08:21:56: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Tue, 16 Jun 2020 08:21:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:56: #2 predicted fragment length is 179 bps INFO @ Tue, 16 Jun 2020 08:21:56: #2 alternative fragment length(s) may be 179 bps INFO @ Tue, 16 Jun 2020 08:21:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.10_model.r WARNING @ Tue, 16 Jun 2020 08:21:56: #2 Since the d (179) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:21:56: #2 You may need to consider one of the other alternative d(s): 179 WARNING @ Tue, 16 Jun 2020 08:21:56: #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 08:21:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:56: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:22:03: 12000000 INFO @ Tue, 16 Jun 2020 08:22:10: 13000000 INFO @ Tue, 16 Jun 2020 08:22:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:16: 14000000 INFO @ Tue, 16 Jun 2020 08:22:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.10_summits.bed INFO @ Tue, 16 Jun 2020 08:22:18: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (281 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:22:21: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:22:21: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:22:21: #1 total tags in treatment: 6859455 INFO @ Tue, 16 Jun 2020 08:22:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:21: #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 08:22:21: #1 tags after filtering in treatment: 6342605 INFO @ Tue, 16 Jun 2020 08:22:21: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 08:22:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:22: #2 number of paired peaks: 393 WARNING @ Tue, 16 Jun 2020 08:22:22: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Tue, 16 Jun 2020 08:22:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:22: #2 predicted fragment length is 179 bps INFO @ Tue, 16 Jun 2020 08:22:22: #2 alternative fragment length(s) may be 179 bps INFO @ Tue, 16 Jun 2020 08:22:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.20_model.r WARNING @ Tue, 16 Jun 2020 08:22:22: #2 Since the d (179) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:22:22: #2 You may need to consider one of the other alternative d(s): 179 WARNING @ Tue, 16 Jun 2020 08:22:22: #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 08:22:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:22:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2035135/SRX2035135.20_summits.bed INFO @ Tue, 16 Jun 2020 08:22:43: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (150 records, 4 fields): 1 millis CompletedMACS2peakCalling