Job ID = 14521874 SRX = ERX4439565 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3217906 spots for ERR4501494/ERR4501494.sra Written 3217906 spots for ERR4501494/ERR4501494.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: 00:02:27 3217906 reads; of these: 3217906 (100.00%) were paired; of these: 776767 (24.14%) aligned concordantly 0 times 2164418 (67.26%) aligned concordantly exactly 1 time 276721 (8.60%) aligned concordantly >1 times ---- 776767 pairs aligned concordantly 0 times; of these: 322261 (41.49%) aligned discordantly 1 time ---- 454506 pairs aligned 0 times concordantly or discordantly; of these: 909012 mates make up the pairs; of these: 778979 (85.70%) aligned 0 times 44678 (4.92%) aligned exactly 1 time 85355 (9.39%) aligned >1 times 87.90% overall alignment rate Time searching: 00:02:27 Overall time: 00:02:27 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_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] 43761 / 2740778 = 0.0160 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 21:52:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.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 21:52:26: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:52:26: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:52:32: 1000000 INFO @ Sat, 15 Jan 2022 21:52:38: 2000000 INFO @ Sat, 15 Jan 2022 21:52:44: 3000000 INFO @ Sat, 15 Jan 2022 21:52:50: 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 21:52:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.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 21:52:56: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:52:56: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:52:56: 5000000 INFO @ Sat, 15 Jan 2022 21:53:00: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:53:00: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:53:00: #1 total tags in treatment: 2402763 INFO @ Sat, 15 Jan 2022 21:53:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:53:00: #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 21:53:00: #1 tags after filtering in treatment: 2167419 INFO @ Sat, 15 Jan 2022 21:53:00: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Jan 2022 21:53:00: #1 finished! INFO @ Sat, 15 Jan 2022 21:53:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:53:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:53:00: #2 number of paired peaks: 177 WARNING @ Sat, 15 Jan 2022 21:53:00: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sat, 15 Jan 2022 21:53:00: start model_add_line... INFO @ Sat, 15 Jan 2022 21:53:00: start X-correlation... INFO @ Sat, 15 Jan 2022 21:53:00: end of X-cor INFO @ Sat, 15 Jan 2022 21:53:00: #2 finished! INFO @ Sat, 15 Jan 2022 21:53:00: #2 predicted fragment length is 183 bps INFO @ Sat, 15 Jan 2022 21:53:00: #2 alternative fragment length(s) may be 1,113,134,167,183,207,334,562,593 bps INFO @ Sat, 15 Jan 2022 21:53:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.05_model.r WARNING @ Sat, 15 Jan 2022 21:53:00: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:53:00: #2 You may need to consider one of the other alternative d(s): 1,113,134,167,183,207,334,562,593 WARNING @ Sat, 15 Jan 2022 21:53:00: #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 21:53:00: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:53:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:53:03: 1000000 INFO @ Sat, 15 Jan 2022 21:53:04: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:53:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:53:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:53:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.05_summits.bed INFO @ Sat, 15 Jan 2022 21:53:06: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (17 records, 4 fields): 161 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:53:09: 2000000 INFO @ Sat, 15 Jan 2022 21:53:15: 3000000 INFO @ Sat, 15 Jan 2022 21:53:22: 4000000 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 21:53:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.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 21:53:26: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:53:26: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:53:29: 5000000 INFO @ Sat, 15 Jan 2022 21:53:33: 1000000 INFO @ Sat, 15 Jan 2022 21:53:33: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:53:33: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:53:33: #1 total tags in treatment: 2402763 INFO @ Sat, 15 Jan 2022 21:53:33: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:53:33: #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 21:53:33: #1 tags after filtering in treatment: 2167419 INFO @ Sat, 15 Jan 2022 21:53:33: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Jan 2022 21:53:33: #1 finished! INFO @ Sat, 15 Jan 2022 21:53:33: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:53:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:53:33: #2 number of paired peaks: 177 WARNING @ Sat, 15 Jan 2022 21:53:33: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sat, 15 Jan 2022 21:53:33: start model_add_line... INFO @ Sat, 15 Jan 2022 21:53:33: start X-correlation... INFO @ Sat, 15 Jan 2022 21:53:33: end of X-cor INFO @ Sat, 15 Jan 2022 21:53:33: #2 finished! INFO @ Sat, 15 Jan 2022 21:53:33: #2 predicted fragment length is 183 bps INFO @ Sat, 15 Jan 2022 21:53:33: #2 alternative fragment length(s) may be 1,113,134,167,183,207,334,562,593 bps INFO @ Sat, 15 Jan 2022 21:53:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.10_model.r WARNING @ Sat, 15 Jan 2022 21:53:33: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:53:33: #2 You may need to consider one of the other alternative d(s): 1,113,134,167,183,207,334,562,593 WARNING @ Sat, 15 Jan 2022 21:53:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 21:53:33: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:53:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:53:38: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:53:39: 2000000 INFO @ Sat, 15 Jan 2022 21:53:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:53:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:53:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.10_summits.bed INFO @ Sat, 15 Jan 2022 21:53:39: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 125 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:53:45: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:53:52: 4000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:53:59: 5000000 INFO @ Sat, 15 Jan 2022 21:54:03: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:54:03: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:54:03: #1 total tags in treatment: 2402763 INFO @ Sat, 15 Jan 2022 21:54:03: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:54:03: #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 21:54:03: #1 tags after filtering in treatment: 2167419 INFO @ Sat, 15 Jan 2022 21:54:03: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Jan 2022 21:54:03: #1 finished! INFO @ Sat, 15 Jan 2022 21:54:03: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:54:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:54:03: #2 number of paired peaks: 177 WARNING @ Sat, 15 Jan 2022 21:54:03: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sat, 15 Jan 2022 21:54:03: start model_add_line... INFO @ Sat, 15 Jan 2022 21:54:03: start X-correlation... INFO @ Sat, 15 Jan 2022 21:54:03: end of X-cor INFO @ Sat, 15 Jan 2022 21:54:03: #2 finished! INFO @ Sat, 15 Jan 2022 21:54:03: #2 predicted fragment length is 183 bps INFO @ Sat, 15 Jan 2022 21:54:03: #2 alternative fragment length(s) may be 1,113,134,167,183,207,334,562,593 bps INFO @ Sat, 15 Jan 2022 21:54:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.20_model.r WARNING @ Sat, 15 Jan 2022 21:54:03: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:54:03: #2 You may need to consider one of the other alternative d(s): 1,113,134,167,183,207,334,562,593 WARNING @ Sat, 15 Jan 2022 21:54:03: #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 21:54:03: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:54:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:54:08: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:54:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:54:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:54:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439565/ERX4439565.20_summits.bed INFO @ Sat, 15 Jan 2022 21:54:09: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (1 records, 4 fields): 362 millis CompletedMACS2peakCalling