Job ID = 12531646 SRX = SRX4555025 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9038083 spots for SRR7696718/SRR7696718.sra Written 9038083 spots for SRR7696718/SRR7696718.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: 00:10:24 9038083 reads; of these: 9038083 (100.00%) were paired; of these: 498200 (5.51%) aligned concordantly 0 times 3319354 (36.73%) aligned concordantly exactly 1 time 5220529 (57.76%) aligned concordantly >1 times ---- 498200 pairs aligned concordantly 0 times; of these: 31188 (6.26%) aligned discordantly 1 time ---- 467012 pairs aligned 0 times concordantly or discordantly; of these: 934024 mates make up the pairs; of these: 669921 (71.72%) aligned 0 times 142231 (15.23%) aligned exactly 1 time 121872 (13.05%) aligned >1 times 96.29% overall alignment rate Time searching: 00:10:24 Overall time: 00:10:24 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 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 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] 2190805 / 4089524 = 0.5357 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:07:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.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, 17 Apr 2021 09:07:09: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:07:09: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:07:17: 1000000 INFO @ Sat, 17 Apr 2021 09:07:24: 2000000 INFO @ Sat, 17 Apr 2021 09:07:32: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:07:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.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, 17 Apr 2021 09:07:39: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:07:39: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:07:39: 4000000 INFO @ Sat, 17 Apr 2021 09:07:47: 5000000 INFO @ Sat, 17 Apr 2021 09:07:48: 1000000 INFO @ Sat, 17 Apr 2021 09:07:54: 6000000 INFO @ Sat, 17 Apr 2021 09:07:56: 2000000 INFO @ Sat, 17 Apr 2021 09:08:02: 7000000 INFO @ Sat, 17 Apr 2021 09:08:04: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:08:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.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, 17 Apr 2021 09:08:09: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:08:09: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:08:09: 8000000 INFO @ Sat, 17 Apr 2021 09:08:12: 4000000 INFO @ Sat, 17 Apr 2021 09:08:17: 9000000 INFO @ Sat, 17 Apr 2021 09:08:20: 5000000 INFO @ Sat, 17 Apr 2021 09:08:21: 1000000 INFO @ Sat, 17 Apr 2021 09:08:25: 10000000 INFO @ Sat, 17 Apr 2021 09:08:28: 6000000 INFO @ Sat, 17 Apr 2021 09:08:32: 11000000 INFO @ Sat, 17 Apr 2021 09:08:33: 2000000 INFO @ Sat, 17 Apr 2021 09:08:35: 7000000 INFO @ Sat, 17 Apr 2021 09:08:41: 12000000 INFO @ Sat, 17 Apr 2021 09:08:43: 8000000 INFO @ Sat, 17 Apr 2021 09:08:45: 3000000 INFO @ Sat, 17 Apr 2021 09:08:49: 13000000 INFO @ Sat, 17 Apr 2021 09:08:49: #1 tag size is determined as 90 bps INFO @ Sat, 17 Apr 2021 09:08:49: #1 tag size = 90 INFO @ Sat, 17 Apr 2021 09:08:49: #1 total tags in treatment: 6352553 INFO @ Sat, 17 Apr 2021 09:08:49: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:08:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:08:49: #1 tags after filtering in treatment: 1418483 INFO @ Sat, 17 Apr 2021 09:08:49: #1 Redundant rate of treatment: 0.78 INFO @ Sat, 17 Apr 2021 09:08:49: #1 finished! INFO @ Sat, 17 Apr 2021 09:08:49: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:08:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:08:49: #2 number of paired peaks: 289 WARNING @ Sat, 17 Apr 2021 09:08:49: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Sat, 17 Apr 2021 09:08:49: start model_add_line... INFO @ Sat, 17 Apr 2021 09:08:49: start X-correlation... INFO @ Sat, 17 Apr 2021 09:08:49: end of X-cor INFO @ Sat, 17 Apr 2021 09:08:49: #2 finished! INFO @ Sat, 17 Apr 2021 09:08:49: #2 predicted fragment length is 58 bps INFO @ Sat, 17 Apr 2021 09:08:49: #2 alternative fragment length(s) may be 4,58 bps INFO @ Sat, 17 Apr 2021 09:08:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.05_model.r WARNING @ Sat, 17 Apr 2021 09:08:49: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:08:49: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Sat, 17 Apr 2021 09:08:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 09:08:49: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:08:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:08:51: 9000000 INFO @ Sat, 17 Apr 2021 09:08:53: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:08:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.05_peaks.xls INFO @ Sat, 17 Apr 2021 09:08:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:08:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.05_summits.bed INFO @ Sat, 17 Apr 2021 09:08:54: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (2299 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:08:56: 4000000 INFO @ Sat, 17 Apr 2021 09:08:58: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 09:09:06: 11000000 INFO @ Sat, 17 Apr 2021 09:09:07: 5000000 BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 09:09:13: 12000000 INFO @ Sat, 17 Apr 2021 09:09:17: 6000000 INFO @ Sat, 17 Apr 2021 09:09:21: 13000000 INFO @ Sat, 17 Apr 2021 09:09:22: #1 tag size is determined as 90 bps INFO @ Sat, 17 Apr 2021 09:09:22: #1 tag size = 90 INFO @ Sat, 17 Apr 2021 09:09:22: #1 total tags in treatment: 6352553 INFO @ Sat, 17 Apr 2021 09:09:22: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:09:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:09:22: #1 tags after filtering in treatment: 1418483 INFO @ Sat, 17 Apr 2021 09:09:22: #1 Redundant rate of treatment: 0.78 INFO @ Sat, 17 Apr 2021 09:09:22: #1 finished! INFO @ Sat, 17 Apr 2021 09:09:22: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:09:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:09:22: #2 number of paired peaks: 289 WARNING @ Sat, 17 Apr 2021 09:09:22: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Sat, 17 Apr 2021 09:09:22: start model_add_line... INFO @ Sat, 17 Apr 2021 09:09:22: start X-correlation... INFO @ Sat, 17 Apr 2021 09:09:22: end of X-cor INFO @ Sat, 17 Apr 2021 09:09:22: #2 finished! INFO @ Sat, 17 Apr 2021 09:09:22: #2 predicted fragment length is 58 bps INFO @ Sat, 17 Apr 2021 09:09:22: #2 alternative fragment length(s) may be 4,58 bps INFO @ Sat, 17 Apr 2021 09:09:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.10_model.r WARNING @ Sat, 17 Apr 2021 09:09:22: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:09:22: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Sat, 17 Apr 2021 09:09:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 09:09:22: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:09:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:09:26: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:09:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.10_peaks.xls INFO @ Sat, 17 Apr 2021 09:09:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:09:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.10_summits.bed INFO @ Sat, 17 Apr 2021 09:09:27: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (1279 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:09:28: 7000000 INFO @ Sat, 17 Apr 2021 09:09:39: 8000000 INFO @ Sat, 17 Apr 2021 09:09:49: 9000000 INFO @ Sat, 17 Apr 2021 09:10:00: 10000000 INFO @ Sat, 17 Apr 2021 09:10:10: 11000000 INFO @ Sat, 17 Apr 2021 09:10:22: 12000000 INFO @ Sat, 17 Apr 2021 09:10:33: 13000000 INFO @ Sat, 17 Apr 2021 09:10:33: #1 tag size is determined as 90 bps INFO @ Sat, 17 Apr 2021 09:10:33: #1 tag size = 90 INFO @ Sat, 17 Apr 2021 09:10:33: #1 total tags in treatment: 6352553 INFO @ Sat, 17 Apr 2021 09:10:33: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:10:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:10:33: #1 tags after filtering in treatment: 1418483 INFO @ Sat, 17 Apr 2021 09:10:33: #1 Redundant rate of treatment: 0.78 INFO @ Sat, 17 Apr 2021 09:10:33: #1 finished! INFO @ Sat, 17 Apr 2021 09:10:33: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:10:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:10:33: #2 number of paired peaks: 289 WARNING @ Sat, 17 Apr 2021 09:10:33: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Sat, 17 Apr 2021 09:10:33: start model_add_line... INFO @ Sat, 17 Apr 2021 09:10:33: start X-correlation... INFO @ Sat, 17 Apr 2021 09:10:33: end of X-cor INFO @ Sat, 17 Apr 2021 09:10:33: #2 finished! INFO @ Sat, 17 Apr 2021 09:10:33: #2 predicted fragment length is 58 bps INFO @ Sat, 17 Apr 2021 09:10:33: #2 alternative fragment length(s) may be 4,58 bps INFO @ Sat, 17 Apr 2021 09:10:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.20_model.r WARNING @ Sat, 17 Apr 2021 09:10:33: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:10:33: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Sat, 17 Apr 2021 09:10:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 09:10:33: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:10:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:10:38: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:10:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.20_peaks.xls INFO @ Sat, 17 Apr 2021 09:10:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:10:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555025/SRX4555025.20_summits.bed INFO @ Sat, 17 Apr 2021 09:10:40: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (433 records, 4 fields): 2 millis CompletedMACS2peakCalling