Job ID = 14168877 SRX = ERX3978898 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19829502 spots for ERR3975967/ERR3975967.sra Written 19829502 spots for ERR3975967/ERR3975967.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170081 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:51:12 19829502 reads; of these: 19829502 (100.00%) were paired; of these: 7321979 (36.92%) aligned concordantly 0 times 9961882 (50.24%) aligned concordantly exactly 1 time 2545641 (12.84%) aligned concordantly >1 times ---- 7321979 pairs aligned concordantly 0 times; of these: 565775 (7.73%) aligned discordantly 1 time ---- 6756204 pairs aligned 0 times concordantly or discordantly; of these: 13512408 mates make up the pairs; of these: 6695264 (49.55%) aligned 0 times 4151154 (30.72%) aligned exactly 1 time 2665990 (19.73%) aligned >1 times 83.12% overall alignment rate Time searching: 01:51:12 Overall time: 01:51:12 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 9774440 / 12881122 = 0.7588 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 @ Fri, 10 Dec 2021 23:37:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 10 Dec 2021 23:37:09: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:37:09: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:37:18: 1000000 INFO @ Fri, 10 Dec 2021 23:37:28: 2000000 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 @ Fri, 10 Dec 2021 23:37:37: 3000000 INFO @ Fri, 10 Dec 2021 23:37:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 10 Dec 2021 23:37:39: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:37:39: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:37:47: 4000000 INFO @ Fri, 10 Dec 2021 23:37:49: 1000000 INFO @ Fri, 10 Dec 2021 23:37:57: 5000000 INFO @ Fri, 10 Dec 2021 23:37:59: 2000000 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 @ Fri, 10 Dec 2021 23:38:07: 6000000 INFO @ Fri, 10 Dec 2021 23:38:09: 3000000 INFO @ Fri, 10 Dec 2021 23:38:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 10 Dec 2021 23:38:09: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:38:09: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:38:17: 7000000 INFO @ Fri, 10 Dec 2021 23:38:20: 4000000 INFO @ Fri, 10 Dec 2021 23:38:20: 1000000 INFO @ Fri, 10 Dec 2021 23:38:29: 8000000 INFO @ Fri, 10 Dec 2021 23:38:31: 2000000 INFO @ Fri, 10 Dec 2021 23:38:32: 5000000 INFO @ Fri, 10 Dec 2021 23:38:41: 3000000 INFO @ Fri, 10 Dec 2021 23:38:41: 9000000 INFO @ Fri, 10 Dec 2021 23:38:44: 6000000 INFO @ Fri, 10 Dec 2021 23:38:53: 4000000 INFO @ Fri, 10 Dec 2021 23:38:53: 10000000 INFO @ Fri, 10 Dec 2021 23:38:56: 7000000 INFO @ Fri, 10 Dec 2021 23:39:04: 11000000 INFO @ Fri, 10 Dec 2021 23:39:05: 5000000 INFO @ Fri, 10 Dec 2021 23:39:07: 8000000 INFO @ Fri, 10 Dec 2021 23:39:16: 12000000 INFO @ Fri, 10 Dec 2021 23:39:16: 6000000 INFO @ Fri, 10 Dec 2021 23:39:18: 9000000 INFO @ Fri, 10 Dec 2021 23:39:28: 13000000 INFO @ Fri, 10 Dec 2021 23:39:28: 7000000 INFO @ Fri, 10 Dec 2021 23:39:29: 10000000 INFO @ Fri, 10 Dec 2021 23:39:33: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 23:39:33: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 23:39:33: #1 total tags in treatment: 3052814 INFO @ Fri, 10 Dec 2021 23:39:33: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:39:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 23:39:33: #1 tags after filtering in treatment: 2844136 INFO @ Fri, 10 Dec 2021 23:39:33: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 23:39:33: #1 finished! INFO @ Fri, 10 Dec 2021 23:39:33: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:39:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:39:33: #2 number of paired peaks: 692 WARNING @ Fri, 10 Dec 2021 23:39:33: Fewer paired peaks (692) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 692 pairs to build model! INFO @ Fri, 10 Dec 2021 23:39:33: start model_add_line... INFO @ Fri, 10 Dec 2021 23:39:33: start X-correlation... INFO @ Fri, 10 Dec 2021 23:39:33: end of X-cor INFO @ Fri, 10 Dec 2021 23:39:33: #2 finished! INFO @ Fri, 10 Dec 2021 23:39:33: #2 predicted fragment length is 122 bps INFO @ Fri, 10 Dec 2021 23:39:33: #2 alternative fragment length(s) may be 122 bps INFO @ Fri, 10 Dec 2021 23:39:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.05_model.r WARNING @ Fri, 10 Dec 2021 23:39:33: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 23:39:33: #2 You may need to consider one of the other alternative d(s): 122 WARNING @ Fri, 10 Dec 2021 23:39:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 23:39:33: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:39:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 23:39:39: 11000000 INFO @ Fri, 10 Dec 2021 23:39:39: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 23:39:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:39:48: 12000000 INFO @ Fri, 10 Dec 2021 23:39:48: 9000000 INFO @ Fri, 10 Dec 2021 23:39:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.05_peaks.xls INFO @ Fri, 10 Dec 2021 23:39:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:39:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.05_summits.bed INFO @ Fri, 10 Dec 2021 23:39:49: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1978 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 23:39:59: 13000000 INFO @ Fri, 10 Dec 2021 23:39:59: 10000000 INFO @ Fri, 10 Dec 2021 23:40:03: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 23:40:03: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 23:40:03: #1 total tags in treatment: 3052814 INFO @ Fri, 10 Dec 2021 23:40:03: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:40:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 23:40:03: #1 tags after filtering in treatment: 2844136 INFO @ Fri, 10 Dec 2021 23:40:03: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 23:40:03: #1 finished! INFO @ Fri, 10 Dec 2021 23:40:03: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:40:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:40:04: #2 number of paired peaks: 692 WARNING @ Fri, 10 Dec 2021 23:40:04: Fewer paired peaks (692) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 692 pairs to build model! INFO @ Fri, 10 Dec 2021 23:40:04: start model_add_line... INFO @ Fri, 10 Dec 2021 23:40:04: start X-correlation... INFO @ Fri, 10 Dec 2021 23:40:04: end of X-cor INFO @ Fri, 10 Dec 2021 23:40:04: #2 finished! INFO @ Fri, 10 Dec 2021 23:40:04: #2 predicted fragment length is 122 bps INFO @ Fri, 10 Dec 2021 23:40:04: #2 alternative fragment length(s) may be 122 bps INFO @ Fri, 10 Dec 2021 23:40:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.10_model.r WARNING @ Fri, 10 Dec 2021 23:40:04: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 23:40:04: #2 You may need to consider one of the other alternative d(s): 122 WARNING @ Fri, 10 Dec 2021 23:40:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 23:40:04: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:40:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 23:40:09: 11000000 INFO @ Fri, 10 Dec 2021 23:40:14: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:40:19: 12000000 INFO @ Fri, 10 Dec 2021 23:40:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.10_peaks.xls INFO @ Fri, 10 Dec 2021 23:40:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:40:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.10_summits.bed INFO @ Fri, 10 Dec 2021 23:40:19: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (719 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 23:40:28: 13000000 INFO @ Fri, 10 Dec 2021 23:40:31: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 23:40:31: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 23:40:31: #1 total tags in treatment: 3052814 INFO @ Fri, 10 Dec 2021 23:40:31: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:40:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 23:40:31: #1 tags after filtering in treatment: 2844136 INFO @ Fri, 10 Dec 2021 23:40:31: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 23:40:31: #1 finished! INFO @ Fri, 10 Dec 2021 23:40:31: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:40:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:40:32: #2 number of paired peaks: 692 WARNING @ Fri, 10 Dec 2021 23:40:32: Fewer paired peaks (692) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 692 pairs to build model! INFO @ Fri, 10 Dec 2021 23:40:32: start model_add_line... INFO @ Fri, 10 Dec 2021 23:40:32: start X-correlation... INFO @ Fri, 10 Dec 2021 23:40:32: end of X-cor INFO @ Fri, 10 Dec 2021 23:40:32: #2 finished! INFO @ Fri, 10 Dec 2021 23:40:32: #2 predicted fragment length is 122 bps INFO @ Fri, 10 Dec 2021 23:40:32: #2 alternative fragment length(s) may be 122 bps INFO @ Fri, 10 Dec 2021 23:40:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.20_model.r WARNING @ Fri, 10 Dec 2021 23:40:32: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 23:40:32: #2 You may need to consider one of the other alternative d(s): 122 WARNING @ Fri, 10 Dec 2021 23:40:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 23:40:32: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:40:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 23:40:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:40:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.20_peaks.xls INFO @ Fri, 10 Dec 2021 23:40:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:40:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978898/ERX3978898.20_summits.bed INFO @ Fri, 10 Dec 2021 23:40:46: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (332 records, 4 fields): 2 millis CompletedMACS2peakCalling