Job ID = 14521232 SRX = SRX8245387 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10006405 spots for SRR11684598/SRR11684598.sra Written 10006405 spots for SRR11684598/SRR11684598.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: 00:05:47 10006405 reads; of these: 10006405 (100.00%) were paired; of these: 5413604 (54.10%) aligned concordantly 0 times 4004464 (40.02%) aligned concordantly exactly 1 time 588337 (5.88%) aligned concordantly >1 times ---- 5413604 pairs aligned concordantly 0 times; of these: 16022 (0.30%) aligned discordantly 1 time ---- 5397582 pairs aligned 0 times concordantly or discordantly; of these: 10795164 mates make up the pairs; of these: 6197534 (57.41%) aligned 0 times 3965023 (36.73%) aligned exactly 1 time 632607 (5.86%) aligned >1 times 69.03% overall alignment rate Time searching: 00:05:47 Overall time: 00:05:47 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] 201622 / 4608073 = 0.0438 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 20:55:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.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 20:55:20: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:55:20: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:55:24: 1000000 INFO @ Sat, 15 Jan 2022 20:55:28: 2000000 INFO @ Sat, 15 Jan 2022 20:55:33: 3000000 INFO @ Sat, 15 Jan 2022 20:55:37: 4000000 INFO @ Sat, 15 Jan 2022 20:55:41: 5000000 INFO @ Sat, 15 Jan 2022 20:55:45: 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 20:55:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.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 20:55:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:55:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:55:50: 7000000 INFO @ Sat, 15 Jan 2022 20:55:54: 1000000 INFO @ Sat, 15 Jan 2022 20:55:54: 8000000 INFO @ Sat, 15 Jan 2022 20:55:58: 2000000 INFO @ Sat, 15 Jan 2022 20:56:00: 9000000 INFO @ Sat, 15 Jan 2022 20:56:02: 3000000 INFO @ Sat, 15 Jan 2022 20:56:05: 10000000 INFO @ Sat, 15 Jan 2022 20:56:07: 4000000 INFO @ Sat, 15 Jan 2022 20:56:10: 11000000 INFO @ Sat, 15 Jan 2022 20:56:11: 5000000 INFO @ Sat, 15 Jan 2022 20:56:14: 12000000 INFO @ Sat, 15 Jan 2022 20:56:15: 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 20:56:19: 13000000 INFO @ Sat, 15 Jan 2022 20:56:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.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 20:56:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:56:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:56:20: 7000000 INFO @ Sat, 15 Jan 2022 20:56:21: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:56:21: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:56:21: #1 total tags in treatment: 4391643 INFO @ Sat, 15 Jan 2022 20:56:21: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:56:21: #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 20:56:21: #1 tags after filtering in treatment: 2695472 INFO @ Sat, 15 Jan 2022 20:56:21: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 15 Jan 2022 20:56:21: #1 finished! INFO @ Sat, 15 Jan 2022 20:56:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:56:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:56:21: #2 number of paired peaks: 170 WARNING @ Sat, 15 Jan 2022 20:56:21: 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 20:56:21: start model_add_line... INFO @ Sat, 15 Jan 2022 20:56:21: start X-correlation... INFO @ Sat, 15 Jan 2022 20:56:21: end of X-cor INFO @ Sat, 15 Jan 2022 20:56:21: #2 finished! INFO @ Sat, 15 Jan 2022 20:56:21: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Jan 2022 20:56:21: #2 alternative fragment length(s) may be 51,74,117,187,202,241,267,274,299,346,363,399,417,495,531,565,588 bps INFO @ Sat, 15 Jan 2022 20:56:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.05_model.r WARNING @ Sat, 15 Jan 2022 20:56:21: #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 20:56:21: #2 You may need to consider one of the other alternative d(s): 51,74,117,187,202,241,267,274,299,346,363,399,417,495,531,565,588 WARNING @ Sat, 15 Jan 2022 20:56:21: #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 20:56:21: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:56:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:56:24: 1000000 INFO @ Sat, 15 Jan 2022 20:56:25: 8000000 INFO @ Sat, 15 Jan 2022 20:56:25: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:56:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:56:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:56:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.05_summits.bed INFO @ Sat, 15 Jan 2022 20:56:28: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (69 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:56:28: 2000000 INFO @ Sat, 15 Jan 2022 20:56:30: 9000000 INFO @ Sat, 15 Jan 2022 20:56:33: 3000000 INFO @ Sat, 15 Jan 2022 20:56:35: 10000000 INFO @ Sat, 15 Jan 2022 20:56:37: 4000000 INFO @ Sat, 15 Jan 2022 20:56:40: 11000000 INFO @ Sat, 15 Jan 2022 20:56:42: 5000000 INFO @ Sat, 15 Jan 2022 20:56:44: 12000000 INFO @ Sat, 15 Jan 2022 20:56:46: 6000000 INFO @ Sat, 15 Jan 2022 20:56:49: 13000000 INFO @ Sat, 15 Jan 2022 20:56:50: 7000000 INFO @ Sat, 15 Jan 2022 20:56:51: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:56:51: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:56:51: #1 total tags in treatment: 4391643 INFO @ Sat, 15 Jan 2022 20:56:51: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:56:51: #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 20:56:51: #1 tags after filtering in treatment: 2695472 INFO @ Sat, 15 Jan 2022 20:56:51: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 15 Jan 2022 20:56:51: #1 finished! INFO @ Sat, 15 Jan 2022 20:56:51: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:56:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:56:51: #2 number of paired peaks: 170 WARNING @ Sat, 15 Jan 2022 20:56:51: 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 20:56:51: start model_add_line... INFO @ Sat, 15 Jan 2022 20:56:51: start X-correlation... INFO @ Sat, 15 Jan 2022 20:56:51: end of X-cor INFO @ Sat, 15 Jan 2022 20:56:51: #2 finished! INFO @ Sat, 15 Jan 2022 20:56:51: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Jan 2022 20:56:51: #2 alternative fragment length(s) may be 51,74,117,187,202,241,267,274,299,346,363,399,417,495,531,565,588 bps INFO @ Sat, 15 Jan 2022 20:56:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.10_model.r WARNING @ Sat, 15 Jan 2022 20:56:51: #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 20:56:51: #2 You may need to consider one of the other alternative d(s): 51,74,117,187,202,241,267,274,299,346,363,399,417,495,531,565,588 WARNING @ Sat, 15 Jan 2022 20:56:51: #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 20:56:51: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:56:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:56:55: 8000000 INFO @ Sat, 15 Jan 2022 20:56:55: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:56:57: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:56:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:56:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.10_summits.bed INFO @ Sat, 15 Jan 2022 20:56:57: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (8 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:57:00: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:57:05: 10000000 INFO @ Sat, 15 Jan 2022 20:57:10: 11000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:57:14: 12000000 INFO @ Sat, 15 Jan 2022 20:57:19: 13000000 INFO @ Sat, 15 Jan 2022 20:57:21: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:57:21: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:57:21: #1 total tags in treatment: 4391643 INFO @ Sat, 15 Jan 2022 20:57:21: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:57:21: #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 20:57:21: #1 tags after filtering in treatment: 2695472 INFO @ Sat, 15 Jan 2022 20:57:21: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 15 Jan 2022 20:57:21: #1 finished! INFO @ Sat, 15 Jan 2022 20:57:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:57:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:57:21: #2 number of paired peaks: 170 WARNING @ Sat, 15 Jan 2022 20:57:21: 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 20:57:21: start model_add_line... INFO @ Sat, 15 Jan 2022 20:57:21: start X-correlation... INFO @ Sat, 15 Jan 2022 20:57:21: end of X-cor INFO @ Sat, 15 Jan 2022 20:57:21: #2 finished! INFO @ Sat, 15 Jan 2022 20:57:21: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Jan 2022 20:57:21: #2 alternative fragment length(s) may be 51,74,117,187,202,241,267,274,299,346,363,399,417,495,531,565,588 bps INFO @ Sat, 15 Jan 2022 20:57:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.20_model.r WARNING @ Sat, 15 Jan 2022 20:57:21: #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 20:57:21: #2 You may need to consider one of the other alternative d(s): 51,74,117,187,202,241,267,274,299,346,363,399,417,495,531,565,588 WARNING @ Sat, 15 Jan 2022 20:57:21: #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 20:57:21: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:57:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:57:25: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:57:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:57:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:57:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245387/SRX8245387.20_summits.bed INFO @ Sat, 15 Jan 2022 20:57:27: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 2 millis CompletedMACS2peakCalling