Job ID = 14521261 SRX = SRX8245390 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10819144 spots for SRR11684601/SRR11684601.sra Written 10819144 spots for SRR11684601/SRR11684601.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: 00:09:27 10819144 reads; of these: 10819144 (100.00%) were paired; of these: 5752578 (53.17%) aligned concordantly 0 times 4417344 (40.83%) aligned concordantly exactly 1 time 649222 (6.00%) aligned concordantly >1 times ---- 5752578 pairs aligned concordantly 0 times; of these: 11504 (0.20%) aligned discordantly 1 time ---- 5741074 pairs aligned 0 times concordantly or discordantly; of these: 11482148 mates make up the pairs; of these: 6453973 (56.21%) aligned 0 times 4344082 (37.83%) aligned exactly 1 time 684093 (5.96%) aligned >1 times 70.17% overall alignment rate Time searching: 00:09:27 Overall time: 00:09:27 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] 243103 / 5077285 = 0.0479 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 21:01:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.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 21:01:00: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:01:00: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:01:06: 1000000 INFO @ Sat, 15 Jan 2022 21:01:12: 2000000 INFO @ Sat, 15 Jan 2022 21:01:18: 3000000 INFO @ Sat, 15 Jan 2022 21:01:24: 4000000 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 21:01:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.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 21:01:30: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:01:30: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:01:30: 5000000 INFO @ Sat, 15 Jan 2022 21:01:36: 6000000 INFO @ Sat, 15 Jan 2022 21:01:36: 1000000 INFO @ Sat, 15 Jan 2022 21:01:42: 7000000 INFO @ Sat, 15 Jan 2022 21:01:43: 2000000 INFO @ Sat, 15 Jan 2022 21:01:48: 8000000 INFO @ Sat, 15 Jan 2022 21:01:48: 3000000 INFO @ Sat, 15 Jan 2022 21:01:54: 4000000 INFO @ Sat, 15 Jan 2022 21:01:54: 9000000 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 21:02:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.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 21:02:00: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:02:00: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:02:00: 5000000 INFO @ Sat, 15 Jan 2022 21:02:01: 10000000 INFO @ Sat, 15 Jan 2022 21:02:06: 6000000 INFO @ Sat, 15 Jan 2022 21:02:07: 11000000 INFO @ Sat, 15 Jan 2022 21:02:07: 1000000 INFO @ Sat, 15 Jan 2022 21:02:12: 7000000 INFO @ Sat, 15 Jan 2022 21:02:13: 12000000 INFO @ Sat, 15 Jan 2022 21:02:14: 2000000 INFO @ Sat, 15 Jan 2022 21:02:18: 8000000 INFO @ Sat, 15 Jan 2022 21:02:19: 13000000 INFO @ Sat, 15 Jan 2022 21:02:21: 3000000 INFO @ Sat, 15 Jan 2022 21:02:24: 9000000 INFO @ Sat, 15 Jan 2022 21:02:25: 14000000 INFO @ Sat, 15 Jan 2022 21:02:28: 4000000 INFO @ Sat, 15 Jan 2022 21:02:29: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:02:29: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:02:29: #1 total tags in treatment: 4823947 INFO @ Sat, 15 Jan 2022 21:02:29: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:02:29: #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 21:02:29: #1 tags after filtering in treatment: 2889113 INFO @ Sat, 15 Jan 2022 21:02:29: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 15 Jan 2022 21:02:29: #1 finished! INFO @ Sat, 15 Jan 2022 21:02:29: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:02:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:02:29: #2 number of paired peaks: 170 WARNING @ Sat, 15 Jan 2022 21:02:29: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 15 Jan 2022 21:02:29: start model_add_line... INFO @ Sat, 15 Jan 2022 21:02:29: start X-correlation... INFO @ Sat, 15 Jan 2022 21:02:29: end of X-cor INFO @ Sat, 15 Jan 2022 21:02:29: #2 finished! INFO @ Sat, 15 Jan 2022 21:02:29: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Jan 2022 21:02:29: #2 alternative fragment length(s) may be 21,51,96,102,135,141,143,185,203,222,252,270,275,304,340,416,419,427,488,497,540,563,579 bps INFO @ Sat, 15 Jan 2022 21:02:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.05_model.r WARNING @ Sat, 15 Jan 2022 21:02:29: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:02:29: #2 You may need to consider one of the other alternative d(s): 21,51,96,102,135,141,143,185,203,222,252,270,275,304,340,416,419,427,488,497,540,563,579 WARNING @ Sat, 15 Jan 2022 21:02:29: #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 21:02:29: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:02:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:02:29: 10000000 INFO @ Sat, 15 Jan 2022 21:02:33: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:02:34: 5000000 INFO @ Sat, 15 Jan 2022 21:02:34: 11000000 INFO @ Sat, 15 Jan 2022 21:02:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:02:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:02:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.05_summits.bed INFO @ Sat, 15 Jan 2022 21:02:36: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (68 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:02:39: 12000000 INFO @ Sat, 15 Jan 2022 21:02:40: 6000000 INFO @ Sat, 15 Jan 2022 21:02:45: 13000000 INFO @ Sat, 15 Jan 2022 21:02:47: 7000000 INFO @ Sat, 15 Jan 2022 21:02:50: 14000000 INFO @ Sat, 15 Jan 2022 21:02:53: 8000000 INFO @ Sat, 15 Jan 2022 21:02:54: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:02:54: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:02:54: #1 total tags in treatment: 4823947 INFO @ Sat, 15 Jan 2022 21:02:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:02:54: #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 21:02:54: #1 tags after filtering in treatment: 2889113 INFO @ Sat, 15 Jan 2022 21:02:54: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 15 Jan 2022 21:02:54: #1 finished! INFO @ Sat, 15 Jan 2022 21:02:54: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:02:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:02:54: #2 number of paired peaks: 170 WARNING @ Sat, 15 Jan 2022 21:02:54: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 15 Jan 2022 21:02:54: start model_add_line... INFO @ Sat, 15 Jan 2022 21:02:54: start X-correlation... INFO @ Sat, 15 Jan 2022 21:02:54: end of X-cor INFO @ Sat, 15 Jan 2022 21:02:54: #2 finished! INFO @ Sat, 15 Jan 2022 21:02:54: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Jan 2022 21:02:54: #2 alternative fragment length(s) may be 21,51,96,102,135,141,143,185,203,222,252,270,275,304,340,416,419,427,488,497,540,563,579 bps INFO @ Sat, 15 Jan 2022 21:02:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.10_model.r WARNING @ Sat, 15 Jan 2022 21:02:54: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:02:54: #2 You may need to consider one of the other alternative d(s): 21,51,96,102,135,141,143,185,203,222,252,270,275,304,340,416,419,427,488,497,540,563,579 WARNING @ Sat, 15 Jan 2022 21:02:54: #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 21:02:54: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:02:54: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:02:58: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:03:00: 9000000 INFO @ Sat, 15 Jan 2022 21:03:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:03:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:03:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.10_summits.bed INFO @ Sat, 15 Jan 2022 21:03:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:03:06: 10000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:03:12: 11000000 INFO @ Sat, 15 Jan 2022 21:03:19: 12000000 INFO @ Sat, 15 Jan 2022 21:03:25: 13000000 INFO @ Sat, 15 Jan 2022 21:03:31: 14000000 INFO @ Sat, 15 Jan 2022 21:03:35: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:03:35: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:03:35: #1 total tags in treatment: 4823947 INFO @ Sat, 15 Jan 2022 21:03:35: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:03:35: #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 21:03:35: #1 tags after filtering in treatment: 2889113 INFO @ Sat, 15 Jan 2022 21:03:35: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 15 Jan 2022 21:03:35: #1 finished! INFO @ Sat, 15 Jan 2022 21:03:35: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:03:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:03:36: #2 number of paired peaks: 170 WARNING @ Sat, 15 Jan 2022 21:03:36: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 15 Jan 2022 21:03:36: start model_add_line... INFO @ Sat, 15 Jan 2022 21:03:36: start X-correlation... INFO @ Sat, 15 Jan 2022 21:03:36: end of X-cor INFO @ Sat, 15 Jan 2022 21:03:36: #2 finished! INFO @ Sat, 15 Jan 2022 21:03:36: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Jan 2022 21:03:36: #2 alternative fragment length(s) may be 21,51,96,102,135,141,143,185,203,222,252,270,275,304,340,416,419,427,488,497,540,563,579 bps INFO @ Sat, 15 Jan 2022 21:03:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.20_model.r WARNING @ Sat, 15 Jan 2022 21:03:36: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:03:36: #2 You may need to consider one of the other alternative d(s): 21,51,96,102,135,141,143,185,203,222,252,270,275,304,340,416,419,427,488,497,540,563,579 WARNING @ Sat, 15 Jan 2022 21:03:36: #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 21:03:36: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:03:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:03:40: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:03:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:03:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:03:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245390/SRX8245390.20_summits.bed INFO @ Sat, 15 Jan 2022 21:03:42: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (3 records, 4 fields): 2 millis CompletedMACS2peakCalling