Job ID = 14521230 SRX = SRX8245385 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7511116 spots for SRR11684596/SRR11684596.sra Written 7511116 spots for SRR11684596/SRR11684596.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: 00:03:56 7511116 reads; of these: 7511116 (100.00%) were paired; of these: 3512347 (46.76%) aligned concordantly 0 times 3549831 (47.26%) aligned concordantly exactly 1 time 448938 (5.98%) aligned concordantly >1 times ---- 3512347 pairs aligned concordantly 0 times; of these: 17921 (0.51%) aligned discordantly 1 time ---- 3494426 pairs aligned 0 times concordantly or discordantly; of these: 6988852 mates make up the pairs; of these: 4056327 (58.04%) aligned 0 times 2563142 (36.67%) aligned exactly 1 time 369383 (5.29%) aligned >1 times 73.00% overall alignment rate Time searching: 00:03:56 Overall time: 00:03:56 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 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 chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 225357 / 4014967 = 0.0561 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:47:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.bam'] # control file = None # effective genome size = 1.21e+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, 15 Jan 2022 20:47:34: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:47:34: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:47:39: 1000000 INFO @ Sat, 15 Jan 2022 20:47:44: 2000000 INFO @ Sat, 15 Jan 2022 20:47:48: 3000000 INFO @ Sat, 15 Jan 2022 20:47:53: 4000000 INFO @ Sat, 15 Jan 2022 20:47:57: 5000000 INFO @ Sat, 15 Jan 2022 20:48:02: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:48:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.bam'] # control file = None # effective genome size = 1.21e+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, 15 Jan 2022 20:48:04: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:48:04: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:48:07: 7000000 INFO @ Sat, 15 Jan 2022 20:48:09: 1000000 INFO @ Sat, 15 Jan 2022 20:48:13: 8000000 INFO @ Sat, 15 Jan 2022 20:48:15: 2000000 INFO @ Sat, 15 Jan 2022 20:48:18: 9000000 INFO @ Sat, 15 Jan 2022 20:48:20: 3000000 INFO @ Sat, 15 Jan 2022 20:48:24: 10000000 INFO @ Sat, 15 Jan 2022 20:48:26: 4000000 INFO @ Sat, 15 Jan 2022 20:48:26: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:48:26: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:48:26: #1 total tags in treatment: 3781221 INFO @ Sat, 15 Jan 2022 20:48:26: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:48:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:48:26: #1 tags after filtering in treatment: 2101510 INFO @ Sat, 15 Jan 2022 20:48:26: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 15 Jan 2022 20:48:26: #1 finished! INFO @ Sat, 15 Jan 2022 20:48:26: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:48:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:48:27: #2 number of paired peaks: 175 WARNING @ Sat, 15 Jan 2022 20:48:27: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 15 Jan 2022 20:48:27: start model_add_line... INFO @ Sat, 15 Jan 2022 20:48:27: start X-correlation... INFO @ Sat, 15 Jan 2022 20:48:27: end of X-cor INFO @ Sat, 15 Jan 2022 20:48:27: #2 finished! INFO @ Sat, 15 Jan 2022 20:48:27: #2 predicted fragment length is 46 bps INFO @ Sat, 15 Jan 2022 20:48:27: #2 alternative fragment length(s) may be 46,70,98,128,172,183,191,219,225,238,244,272,321,342,375,396,413,454,478,506,545,587 bps INFO @ Sat, 15 Jan 2022 20:48:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.05_model.r WARNING @ Sat, 15 Jan 2022 20:48:27: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:48:27: #2 You may need to consider one of the other alternative d(s): 46,70,98,128,172,183,191,219,225,238,244,272,321,342,375,396,413,454,478,506,545,587 WARNING @ Sat, 15 Jan 2022 20:48:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 20:48:27: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:48:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:48:30: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:48:31: 5000000 INFO @ Sat, 15 Jan 2022 20:48:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:48:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:48:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.05_summits.bed INFO @ Sat, 15 Jan 2022 20:48:31: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (34 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:48:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.bam'] # control file = None # effective genome size = 1.21e+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, 15 Jan 2022 20:48:34: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:48:34: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:48:36: 6000000 INFO @ Sat, 15 Jan 2022 20:48:39: 1000000 INFO @ Sat, 15 Jan 2022 20:48:41: 7000000 INFO @ Sat, 15 Jan 2022 20:48:45: 2000000 INFO @ Sat, 15 Jan 2022 20:48:47: 8000000 INFO @ Sat, 15 Jan 2022 20:48:50: 3000000 INFO @ Sat, 15 Jan 2022 20:48:52: 9000000 INFO @ Sat, 15 Jan 2022 20:48:56: 4000000 INFO @ Sat, 15 Jan 2022 20:48:58: 10000000 INFO @ Sat, 15 Jan 2022 20:49:00: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:49:00: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:49:00: #1 total tags in treatment: 3781221 INFO @ Sat, 15 Jan 2022 20:49:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:49:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:49:00: #1 tags after filtering in treatment: 2101510 INFO @ Sat, 15 Jan 2022 20:49:00: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 15 Jan 2022 20:49:00: #1 finished! INFO @ Sat, 15 Jan 2022 20:49:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:49:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:49:01: #2 number of paired peaks: 175 WARNING @ Sat, 15 Jan 2022 20:49:01: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 15 Jan 2022 20:49:01: start model_add_line... INFO @ Sat, 15 Jan 2022 20:49:01: start X-correlation... INFO @ Sat, 15 Jan 2022 20:49:01: end of X-cor INFO @ Sat, 15 Jan 2022 20:49:01: #2 finished! INFO @ Sat, 15 Jan 2022 20:49:01: #2 predicted fragment length is 46 bps INFO @ Sat, 15 Jan 2022 20:49:01: #2 alternative fragment length(s) may be 46,70,98,128,172,183,191,219,225,238,244,272,321,342,375,396,413,454,478,506,545,587 bps INFO @ Sat, 15 Jan 2022 20:49:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.10_model.r WARNING @ Sat, 15 Jan 2022 20:49:01: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:49:01: #2 You may need to consider one of the other alternative d(s): 46,70,98,128,172,183,191,219,225,238,244,272,321,342,375,396,413,454,478,506,545,587 WARNING @ Sat, 15 Jan 2022 20:49:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 20:49:01: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:49:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:49:01: 5000000 INFO @ Sat, 15 Jan 2022 20:49:04: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:49:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:49:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:49:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.10_summits.bed INFO @ Sat, 15 Jan 2022 20:49:06: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (7 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:49:06: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:49:11: 7000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:49:16: 8000000 INFO @ Sat, 15 Jan 2022 20:49:21: 9000000 INFO @ Sat, 15 Jan 2022 20:49:26: 10000000 INFO @ Sat, 15 Jan 2022 20:49:29: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:49:29: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:49:29: #1 total tags in treatment: 3781221 INFO @ Sat, 15 Jan 2022 20:49:29: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:49:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:49:29: #1 tags after filtering in treatment: 2101510 INFO @ Sat, 15 Jan 2022 20:49:29: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 15 Jan 2022 20:49:29: #1 finished! INFO @ Sat, 15 Jan 2022 20:49:29: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:49:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:49:29: #2 number of paired peaks: 175 WARNING @ Sat, 15 Jan 2022 20:49:29: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 15 Jan 2022 20:49:29: start model_add_line... INFO @ Sat, 15 Jan 2022 20:49:29: start X-correlation... INFO @ Sat, 15 Jan 2022 20:49:29: end of X-cor INFO @ Sat, 15 Jan 2022 20:49:29: #2 finished! INFO @ Sat, 15 Jan 2022 20:49:29: #2 predicted fragment length is 46 bps INFO @ Sat, 15 Jan 2022 20:49:29: #2 alternative fragment length(s) may be 46,70,98,128,172,183,191,219,225,238,244,272,321,342,375,396,413,454,478,506,545,587 bps INFO @ Sat, 15 Jan 2022 20:49:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.20_model.r WARNING @ Sat, 15 Jan 2022 20:49:29: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:49:29: #2 You may need to consider one of the other alternative d(s): 46,70,98,128,172,183,191,219,225,238,244,272,321,342,375,396,413,454,478,506,545,587 WARNING @ Sat, 15 Jan 2022 20:49:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 20:49:29: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:49:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:49:33: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:49:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:49:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:49:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245385/SRX8245385.20_summits.bed INFO @ Sat, 15 Jan 2022 20:49:34: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling