Job ID = 14168101 SRX = ERX3978826 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12908569 spots for ERR3975895/ERR3975895.sra Written 12908569 spots for ERR3975895/ERR3975895.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169030 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:51:37 12908569 reads; of these: 12908569 (100.00%) were paired; of these: 1448772 (11.22%) aligned concordantly 0 times 9028736 (69.94%) aligned concordantly exactly 1 time 2431061 (18.83%) aligned concordantly >1 times ---- 1448772 pairs aligned concordantly 0 times; of these: 257166 (17.75%) aligned discordantly 1 time ---- 1191606 pairs aligned 0 times concordantly or discordantly; of these: 2383212 mates make up the pairs; of these: 1250421 (52.47%) aligned 0 times 542452 (22.76%) aligned exactly 1 time 590339 (24.77%) aligned >1 times 95.16% overall alignment rate Time searching: 00:51:38 Overall time: 00:51:38 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 12 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] 7066212 / 11673033 = 0.6053 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 16:23:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.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 16:23:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:23:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:23:23: 1000000 INFO @ Fri, 10 Dec 2021 16:23:34: 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 16:23:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.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 16:23:42: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:23:42: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:23:44: 3000000 INFO @ Fri, 10 Dec 2021 16:23:53: 1000000 INFO @ Fri, 10 Dec 2021 16:23:55: 4000000 INFO @ Fri, 10 Dec 2021 16:24:04: 2000000 INFO @ Fri, 10 Dec 2021 16:24:05: 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 @ Fri, 10 Dec 2021 16:24:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.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 16:24:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:24:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:24:15: 3000000 INFO @ Fri, 10 Dec 2021 16:24:16: 6000000 INFO @ Fri, 10 Dec 2021 16:24:23: 1000000 INFO @ Fri, 10 Dec 2021 16:24:25: 4000000 INFO @ Fri, 10 Dec 2021 16:24:27: 7000000 INFO @ Fri, 10 Dec 2021 16:24:34: 2000000 INFO @ Fri, 10 Dec 2021 16:24:35: 5000000 INFO @ Fri, 10 Dec 2021 16:24:38: 8000000 INFO @ Fri, 10 Dec 2021 16:24:45: 3000000 INFO @ Fri, 10 Dec 2021 16:24:46: 6000000 INFO @ Fri, 10 Dec 2021 16:24:50: 9000000 INFO @ Fri, 10 Dec 2021 16:24:56: 4000000 INFO @ Fri, 10 Dec 2021 16:24:56: 7000000 INFO @ Fri, 10 Dec 2021 16:25:01: 10000000 INFO @ Fri, 10 Dec 2021 16:25:06: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:25:06: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:25:06: #1 total tags in treatment: 4542271 INFO @ Fri, 10 Dec 2021 16:25:06: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:25:06: #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 16:25:06: #1 tags after filtering in treatment: 4300519 INFO @ Fri, 10 Dec 2021 16:25:06: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 16:25:06: #1 finished! INFO @ Fri, 10 Dec 2021 16:25:06: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:25:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:25:06: 5000000 INFO @ Fri, 10 Dec 2021 16:25:06: #2 number of paired peaks: 682 WARNING @ Fri, 10 Dec 2021 16:25:06: Fewer paired peaks (682) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 682 pairs to build model! INFO @ Fri, 10 Dec 2021 16:25:06: start model_add_line... INFO @ Fri, 10 Dec 2021 16:25:06: start X-correlation... INFO @ Fri, 10 Dec 2021 16:25:06: end of X-cor INFO @ Fri, 10 Dec 2021 16:25:06: #2 finished! INFO @ Fri, 10 Dec 2021 16:25:06: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Dec 2021 16:25:06: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 10 Dec 2021 16:25:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.05_model.r WARNING @ Fri, 10 Dec 2021 16:25:06: #2 Since the d (155) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:25:06: #2 You may need to consider one of the other alternative d(s): 155 WARNING @ Fri, 10 Dec 2021 16:25:06: #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 16:25:06: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:25:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:25:07: 8000000 INFO @ Fri, 10 Dec 2021 16:25:17: 6000000 INFO @ Fri, 10 Dec 2021 16:25:18: 9000000 INFO @ Fri, 10 Dec 2021 16:25:21: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 16:25:27: 7000000 INFO @ Fri, 10 Dec 2021 16:25:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.05_peaks.xls INFO @ Fri, 10 Dec 2021 16:25:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:25:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.05_summits.bed INFO @ Fri, 10 Dec 2021 16:25:28: Done! INFO @ Fri, 10 Dec 2021 16:25:28: 10000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2922 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:25:33: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:25:33: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:25:33: #1 total tags in treatment: 4542271 INFO @ Fri, 10 Dec 2021 16:25:33: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:25:33: #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 16:25:33: #1 tags after filtering in treatment: 4300519 INFO @ Fri, 10 Dec 2021 16:25:33: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 16:25:33: #1 finished! INFO @ Fri, 10 Dec 2021 16:25:33: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:25:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:25:33: #2 number of paired peaks: 682 WARNING @ Fri, 10 Dec 2021 16:25:33: Fewer paired peaks (682) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 682 pairs to build model! INFO @ Fri, 10 Dec 2021 16:25:33: start model_add_line... INFO @ Fri, 10 Dec 2021 16:25:33: start X-correlation... INFO @ Fri, 10 Dec 2021 16:25:33: end of X-cor INFO @ Fri, 10 Dec 2021 16:25:33: #2 finished! INFO @ Fri, 10 Dec 2021 16:25:33: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Dec 2021 16:25:33: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 10 Dec 2021 16:25:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.10_model.r WARNING @ Fri, 10 Dec 2021 16:25:33: #2 Since the d (155) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:25:33: #2 You may need to consider one of the other alternative d(s): 155 WARNING @ Fri, 10 Dec 2021 16:25:33: #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 16:25:33: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:25:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:25:38: 8000000 INFO @ Fri, 10 Dec 2021 16:25:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:25:49: 9000000 INFO @ Fri, 10 Dec 2021 16:25:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.10_peaks.xls INFO @ Fri, 10 Dec 2021 16:25:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:25:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.10_summits.bed INFO @ Fri, 10 Dec 2021 16:25:54: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1217 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 16:25:59: 10000000 INFO @ Fri, 10 Dec 2021 16:26:03: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:26:03: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:26:03: #1 total tags in treatment: 4542271 INFO @ Fri, 10 Dec 2021 16:26:03: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:26:03: #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 16:26:03: #1 tags after filtering in treatment: 4300519 INFO @ Fri, 10 Dec 2021 16:26:03: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 16:26:03: #1 finished! INFO @ Fri, 10 Dec 2021 16:26:03: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:26:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:26:04: #2 number of paired peaks: 682 WARNING @ Fri, 10 Dec 2021 16:26:04: Fewer paired peaks (682) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 682 pairs to build model! INFO @ Fri, 10 Dec 2021 16:26:04: start model_add_line... INFO @ Fri, 10 Dec 2021 16:26:04: start X-correlation... INFO @ Fri, 10 Dec 2021 16:26:04: end of X-cor INFO @ Fri, 10 Dec 2021 16:26:04: #2 finished! INFO @ Fri, 10 Dec 2021 16:26:04: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Dec 2021 16:26:04: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 10 Dec 2021 16:26:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.20_model.r WARNING @ Fri, 10 Dec 2021 16:26:04: #2 Since the d (155) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:26:04: #2 You may need to consider one of the other alternative d(s): 155 WARNING @ Fri, 10 Dec 2021 16:26:04: #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 16:26:04: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:26:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:26:18: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:26:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.20_peaks.xls INFO @ Fri, 10 Dec 2021 16:26:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:26:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978826/ERX3978826.20_summits.bed INFO @ Fri, 10 Dec 2021 16:26:25: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (532 records, 4 fields): 4 millis CompletedMACS2peakCalling