Job ID = 14520801 SRX = SRX8245528 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9994501 spots for SRR11684739/SRR11684739.sra Written 9994501 spots for SRR11684739/SRR11684739.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: 00:05:30 9994501 reads; of these: 9994501 (100.00%) were paired; of these: 5552930 (55.56%) aligned concordantly 0 times 3915045 (39.17%) aligned concordantly exactly 1 time 526526 (5.27%) aligned concordantly >1 times ---- 5552930 pairs aligned concordantly 0 times; of these: 52659 (0.95%) aligned discordantly 1 time ---- 5500271 pairs aligned 0 times concordantly or discordantly; of these: 11000542 mates make up the pairs; of these: 6084029 (55.31%) aligned 0 times 4281717 (38.92%) aligned exactly 1 time 634796 (5.77%) aligned >1 times 69.56% overall alignment rate Time searching: 00:05:30 Overall time: 00:05:30 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] 83392 / 4493466 = 0.0186 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 20:05:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.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 20:05:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:05:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:05:28: 1000000 INFO @ Sat, 15 Jan 2022 20:05:32: 2000000 INFO @ Sat, 15 Jan 2022 20:05:37: 3000000 INFO @ Sat, 15 Jan 2022 20:05:41: 4000000 INFO @ Sat, 15 Jan 2022 20:05:45: 5000000 INFO @ Sat, 15 Jan 2022 20:05:49: 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 20:05:53: 7000000 INFO @ Sat, 15 Jan 2022 20:05:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.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 20:05:54: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:05:54: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:05:58: 8000000 INFO @ Sat, 15 Jan 2022 20:05:59: 1000000 INFO @ Sat, 15 Jan 2022 20:06:02: 9000000 INFO @ Sat, 15 Jan 2022 20:06:04: 2000000 INFO @ Sat, 15 Jan 2022 20:06:06: 10000000 INFO @ Sat, 15 Jan 2022 20:06:09: 3000000 INFO @ Sat, 15 Jan 2022 20:06:11: 11000000 INFO @ Sat, 15 Jan 2022 20:06:14: 4000000 INFO @ Sat, 15 Jan 2022 20:06:15: 12000000 INFO @ Sat, 15 Jan 2022 20:06:19: 13000000 INFO @ Sat, 15 Jan 2022 20:06:19: 5000000 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 20:06:23: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:06:23: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:06:23: #1 total tags in treatment: 4358416 INFO @ Sat, 15 Jan 2022 20:06:23: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:06:23: #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 20:06:23: #1 tags after filtering in treatment: 3069526 INFO @ Sat, 15 Jan 2022 20:06:23: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 20:06:23: #1 finished! INFO @ Sat, 15 Jan 2022 20:06:23: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:06:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:06:23: #2 number of paired peaks: 169 WARNING @ Sat, 15 Jan 2022 20:06:23: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 15 Jan 2022 20:06:23: start model_add_line... INFO @ Sat, 15 Jan 2022 20:06:23: start X-correlation... INFO @ Sat, 15 Jan 2022 20:06:23: end of X-cor INFO @ Sat, 15 Jan 2022 20:06:23: #2 finished! INFO @ Sat, 15 Jan 2022 20:06:23: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 20:06:23: #2 alternative fragment length(s) may be 20,50,74,88,111,136,138,167,201,249,282,296,311,341,364,392,400,419,444,478,525,585 bps INFO @ Sat, 15 Jan 2022 20:06:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.05_model.r WARNING @ Sat, 15 Jan 2022 20:06:23: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:06:23: #2 You may need to consider one of the other alternative d(s): 20,50,74,88,111,136,138,167,201,249,282,296,311,341,364,392,400,419,444,478,525,585 WARNING @ Sat, 15 Jan 2022 20:06:23: #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 20:06:23: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:06:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:06:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.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 20:06:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:06:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:06:25: 6000000 INFO @ Sat, 15 Jan 2022 20:06:27: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:06:28: 1000000 INFO @ Sat, 15 Jan 2022 20:06:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:06:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:06:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.05_summits.bed INFO @ Sat, 15 Jan 2022 20:06:29: Done! pass1 - making usageList (14 chroms): 1 millis INFO @ Sat, 15 Jan 2022 20:06:30: 7000000 pass2 - checking and writing primary data (27 records, 4 fields): 610 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:06:33: 2000000 INFO @ Sat, 15 Jan 2022 20:06:35: 8000000 INFO @ Sat, 15 Jan 2022 20:06:37: 3000000 INFO @ Sat, 15 Jan 2022 20:06:40: 9000000 INFO @ Sat, 15 Jan 2022 20:06:41: 4000000 INFO @ Sat, 15 Jan 2022 20:06:45: 10000000 INFO @ Sat, 15 Jan 2022 20:06:45: 5000000 INFO @ Sat, 15 Jan 2022 20:06:50: 6000000 INFO @ Sat, 15 Jan 2022 20:06:50: 11000000 INFO @ Sat, 15 Jan 2022 20:06:54: 7000000 INFO @ Sat, 15 Jan 2022 20:06:55: 12000000 INFO @ Sat, 15 Jan 2022 20:06:58: 8000000 INFO @ Sat, 15 Jan 2022 20:07:01: 13000000 INFO @ Sat, 15 Jan 2022 20:07:03: 9000000 INFO @ Sat, 15 Jan 2022 20:07:05: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:07:05: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:07:05: #1 total tags in treatment: 4358416 INFO @ Sat, 15 Jan 2022 20:07:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:07:05: #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 20:07:05: #1 tags after filtering in treatment: 3069526 INFO @ Sat, 15 Jan 2022 20:07:05: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 20:07:05: #1 finished! INFO @ Sat, 15 Jan 2022 20:07:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:07:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:07:05: #2 number of paired peaks: 169 WARNING @ Sat, 15 Jan 2022 20:07:05: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 15 Jan 2022 20:07:05: start model_add_line... INFO @ Sat, 15 Jan 2022 20:07:05: start X-correlation... INFO @ Sat, 15 Jan 2022 20:07:05: end of X-cor INFO @ Sat, 15 Jan 2022 20:07:05: #2 finished! INFO @ Sat, 15 Jan 2022 20:07:05: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 20:07:05: #2 alternative fragment length(s) may be 20,50,74,88,111,136,138,167,201,249,282,296,311,341,364,392,400,419,444,478,525,585 bps INFO @ Sat, 15 Jan 2022 20:07:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.10_model.r WARNING @ Sat, 15 Jan 2022 20:07:05: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:07:05: #2 You may need to consider one of the other alternative d(s): 20,50,74,88,111,136,138,167,201,249,282,296,311,341,364,392,400,419,444,478,525,585 WARNING @ Sat, 15 Jan 2022 20:07:05: #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 20:07:05: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:07:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:07:07: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:07:09: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:07:11: 11000000 INFO @ Sat, 15 Jan 2022 20:07:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:07:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:07:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.10_summits.bed INFO @ Sat, 15 Jan 2022 20:07:11: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:07:15: 12000000 INFO @ Sat, 15 Jan 2022 20:07:20: 13000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:07:23: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:07:23: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:07:23: #1 total tags in treatment: 4358416 INFO @ Sat, 15 Jan 2022 20:07:23: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:07:23: #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 20:07:23: #1 tags after filtering in treatment: 3069526 INFO @ Sat, 15 Jan 2022 20:07:23: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 20:07:23: #1 finished! INFO @ Sat, 15 Jan 2022 20:07:23: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:07:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:07:23: #2 number of paired peaks: 169 WARNING @ Sat, 15 Jan 2022 20:07:23: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 15 Jan 2022 20:07:23: start model_add_line... INFO @ Sat, 15 Jan 2022 20:07:23: start X-correlation... INFO @ Sat, 15 Jan 2022 20:07:23: end of X-cor INFO @ Sat, 15 Jan 2022 20:07:23: #2 finished! INFO @ Sat, 15 Jan 2022 20:07:23: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 20:07:23: #2 alternative fragment length(s) may be 20,50,74,88,111,136,138,167,201,249,282,296,311,341,364,392,400,419,444,478,525,585 bps INFO @ Sat, 15 Jan 2022 20:07:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.20_model.r WARNING @ Sat, 15 Jan 2022 20:07:23: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:07:23: #2 You may need to consider one of the other alternative d(s): 20,50,74,88,111,136,138,167,201,249,282,296,311,341,364,392,400,419,444,478,525,585 WARNING @ Sat, 15 Jan 2022 20:07:23: #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 20:07:23: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:07:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:07:27: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:07:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:07:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:07:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245528/SRX8245528.20_summits.bed INFO @ Sat, 15 Jan 2022 20:07:30: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 21 millis CompletedMACS2peakCalling