Job ID = 14521192 SRX = SRX8245370 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12707292 spots for SRR11684581/SRR11684581.sra Written 12707292 spots for SRR11684581/SRR11684581.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: 00:05:51 12707292 reads; of these: 12707292 (100.00%) were paired; of these: 7242287 (56.99%) aligned concordantly 0 times 4932598 (38.82%) aligned concordantly exactly 1 time 532407 (4.19%) aligned concordantly >1 times ---- 7242287 pairs aligned concordantly 0 times; of these: 129048 (1.78%) aligned discordantly 1 time ---- 7113239 pairs aligned 0 times concordantly or discordantly; of these: 14226478 mates make up the pairs; of these: 9009272 (63.33%) aligned 0 times 4570083 (32.12%) aligned exactly 1 time 647123 (4.55%) aligned >1 times 64.55% overall alignment rate Time searching: 00:05:51 Overall time: 00:05:51 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] 657002 / 5593340 = 0.1175 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 20:48:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.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 20:48:58: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:48:58: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:49:02: 1000000 INFO @ Sat, 15 Jan 2022 20:49:07: 2000000 INFO @ Sat, 15 Jan 2022 20:49:11: 3000000 INFO @ Sat, 15 Jan 2022 20:49:16: 4000000 INFO @ Sat, 15 Jan 2022 20:49:20: 5000000 INFO @ Sat, 15 Jan 2022 20:49:24: 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 20:49:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.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 20:49:28: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:49:28: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:49:29: 7000000 INFO @ Sat, 15 Jan 2022 20:49:32: 1000000 INFO @ Sat, 15 Jan 2022 20:49:33: 8000000 INFO @ Sat, 15 Jan 2022 20:49:37: 2000000 INFO @ Sat, 15 Jan 2022 20:49:38: 9000000 INFO @ Sat, 15 Jan 2022 20:49:41: 3000000 INFO @ Sat, 15 Jan 2022 20:49:42: 10000000 INFO @ Sat, 15 Jan 2022 20:49:46: 4000000 INFO @ Sat, 15 Jan 2022 20:49:47: 11000000 INFO @ Sat, 15 Jan 2022 20:49:50: 5000000 INFO @ Sat, 15 Jan 2022 20:49:51: 12000000 INFO @ Sat, 15 Jan 2022 20:49:55: 6000000 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 20:49:56: 13000000 INFO @ Sat, 15 Jan 2022 20:49:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.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 20:49:58: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:49:58: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:49:59: 7000000 INFO @ Sat, 15 Jan 2022 20:50:01: 14000000 INFO @ Sat, 15 Jan 2022 20:50:03: 1000000 INFO @ Sat, 15 Jan 2022 20:50:04: 8000000 INFO @ Sat, 15 Jan 2022 20:50:06: 15000000 INFO @ Sat, 15 Jan 2022 20:50:06: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:50:06: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:50:06: #1 total tags in treatment: 4813317 INFO @ Sat, 15 Jan 2022 20:50:06: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:50:06: #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 20:50:06: #1 tags after filtering in treatment: 2652801 INFO @ Sat, 15 Jan 2022 20:50:06: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 15 Jan 2022 20:50:06: #1 finished! INFO @ Sat, 15 Jan 2022 20:50:06: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:50:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:50:06: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 20:50:06: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Jan 2022 20:50:06: start model_add_line... INFO @ Sat, 15 Jan 2022 20:50:06: start X-correlation... INFO @ Sat, 15 Jan 2022 20:50:06: end of X-cor INFO @ Sat, 15 Jan 2022 20:50:06: #2 finished! INFO @ Sat, 15 Jan 2022 20:50:06: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 20:50:06: #2 alternative fragment length(s) may be 50,88,103,133,150,209,234,263,283,314,339,367,373,381,398,433,439,488,588 bps INFO @ Sat, 15 Jan 2022 20:50:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.05_model.r WARNING @ Sat, 15 Jan 2022 20:50:06: #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 20:50:06: #2 You may need to consider one of the other alternative d(s): 50,88,103,133,150,209,234,263,283,314,339,367,373,381,398,433,439,488,588 WARNING @ Sat, 15 Jan 2022 20:50:06: #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 20:50:06: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:50:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:50:08: 2000000 INFO @ Sat, 15 Jan 2022 20:50:09: 9000000 INFO @ Sat, 15 Jan 2022 20:50:10: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:50:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:50:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:50:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.05_summits.bed INFO @ Sat, 15 Jan 2022 20:50:12: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (23 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:50:13: 10000000 INFO @ Sat, 15 Jan 2022 20:50:14: 3000000 INFO @ Sat, 15 Jan 2022 20:50:18: 11000000 INFO @ Sat, 15 Jan 2022 20:50:19: 4000000 INFO @ Sat, 15 Jan 2022 20:50:23: 12000000 INFO @ Sat, 15 Jan 2022 20:50:24: 5000000 INFO @ Sat, 15 Jan 2022 20:50:28: 13000000 INFO @ Sat, 15 Jan 2022 20:50:29: 6000000 INFO @ Sat, 15 Jan 2022 20:50:32: 14000000 INFO @ Sat, 15 Jan 2022 20:50:34: 7000000 INFO @ Sat, 15 Jan 2022 20:50:37: 15000000 INFO @ Sat, 15 Jan 2022 20:50:38: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:50:38: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:50:38: #1 total tags in treatment: 4813317 INFO @ Sat, 15 Jan 2022 20:50:38: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:50:38: #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 20:50:38: #1 tags after filtering in treatment: 2652801 INFO @ Sat, 15 Jan 2022 20:50:38: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 15 Jan 2022 20:50:38: #1 finished! INFO @ Sat, 15 Jan 2022 20:50:38: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:50:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:50:38: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 20:50:38: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Jan 2022 20:50:38: start model_add_line... INFO @ Sat, 15 Jan 2022 20:50:38: start X-correlation... INFO @ Sat, 15 Jan 2022 20:50:38: end of X-cor INFO @ Sat, 15 Jan 2022 20:50:38: #2 finished! INFO @ Sat, 15 Jan 2022 20:50:38: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 20:50:38: #2 alternative fragment length(s) may be 50,88,103,133,150,209,234,263,283,314,339,367,373,381,398,433,439,488,588 bps INFO @ Sat, 15 Jan 2022 20:50:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.10_model.r WARNING @ Sat, 15 Jan 2022 20:50:38: #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 20:50:38: #2 You may need to consider one of the other alternative d(s): 50,88,103,133,150,209,234,263,283,314,339,367,373,381,398,433,439,488,588 WARNING @ Sat, 15 Jan 2022 20:50:38: #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 20:50:38: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:50:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:50:39: 8000000 INFO @ Sat, 15 Jan 2022 20:50:42: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:50:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:50:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:50:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.10_summits.bed INFO @ Sat, 15 Jan 2022 20:50:44: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:50:44: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:50:49: 10000000 INFO @ Sat, 15 Jan 2022 20:50:55: 11000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:51:00: 12000000 INFO @ Sat, 15 Jan 2022 20:51:05: 13000000 INFO @ Sat, 15 Jan 2022 20:51:10: 14000000 INFO @ Sat, 15 Jan 2022 20:51:16: 15000000 INFO @ Sat, 15 Jan 2022 20:51:16: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:51:16: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:51:16: #1 total tags in treatment: 4813317 INFO @ Sat, 15 Jan 2022 20:51:16: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:51:16: #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 20:51:16: #1 tags after filtering in treatment: 2652801 INFO @ Sat, 15 Jan 2022 20:51:16: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 15 Jan 2022 20:51:16: #1 finished! INFO @ Sat, 15 Jan 2022 20:51:16: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:51:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:51:16: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 20:51:16: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Jan 2022 20:51:16: start model_add_line... INFO @ Sat, 15 Jan 2022 20:51:16: start X-correlation... INFO @ Sat, 15 Jan 2022 20:51:16: end of X-cor INFO @ Sat, 15 Jan 2022 20:51:16: #2 finished! INFO @ Sat, 15 Jan 2022 20:51:16: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 20:51:16: #2 alternative fragment length(s) may be 50,88,103,133,150,209,234,263,283,314,339,367,373,381,398,433,439,488,588 bps INFO @ Sat, 15 Jan 2022 20:51:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.20_model.r WARNING @ Sat, 15 Jan 2022 20:51:16: #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 20:51:16: #2 You may need to consider one of the other alternative d(s): 50,88,103,133,150,209,234,263,283,314,339,367,373,381,398,433,439,488,588 WARNING @ Sat, 15 Jan 2022 20:51:16: #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 20:51:16: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:51:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:51:20: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:51:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:51:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:51:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245370/SRX8245370.20_summits.bed INFO @ Sat, 15 Jan 2022 20:51:22: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling