Job ID = 14166957 SRX = SRX7541122 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22700914 spots for SRR10871148/SRR10871148.sra Written 22700914 spots for SRR10871148/SRR10871148.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167348 ("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: 00:34:47 22700914 reads; of these: 22700914 (100.00%) were paired; of these: 16566936 (72.98%) aligned concordantly 0 times 3878062 (17.08%) aligned concordantly exactly 1 time 2255916 (9.94%) aligned concordantly >1 times ---- 16566936 pairs aligned concordantly 0 times; of these: 542085 (3.27%) aligned discordantly 1 time ---- 16024851 pairs aligned 0 times concordantly or discordantly; of these: 32049702 mates make up the pairs; of these: 30169956 (94.13%) aligned 0 times 1022112 (3.19%) aligned exactly 1 time 857634 (2.68%) aligned >1 times 33.55% overall alignment rate Time searching: 00:34:47 Overall time: 00:34:47 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 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] 1443461 / 6578002 = 0.2194 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 08:49:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.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 08:49:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:49:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:49:20: 1000000 INFO @ Fri, 10 Dec 2021 08:49:27: 2000000 INFO @ Fri, 10 Dec 2021 08:49:34: 3000000 INFO @ Fri, 10 Dec 2021 08:49:40: 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 @ Fri, 10 Dec 2021 08:49:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.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 08:49:43: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:49:43: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:49:48: 5000000 INFO @ Fri, 10 Dec 2021 08:49:52: 1000000 INFO @ Fri, 10 Dec 2021 08:49:56: 6000000 INFO @ Fri, 10 Dec 2021 08:50:01: 2000000 INFO @ Fri, 10 Dec 2021 08:50:04: 7000000 INFO @ Fri, 10 Dec 2021 08:50:10: 3000000 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 08:50:12: 8000000 INFO @ Fri, 10 Dec 2021 08:50:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.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 08:50:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:50:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:50:19: 4000000 INFO @ Fri, 10 Dec 2021 08:50:21: 9000000 INFO @ Fri, 10 Dec 2021 08:50:23: 1000000 INFO @ Fri, 10 Dec 2021 08:50:29: 10000000 INFO @ Fri, 10 Dec 2021 08:50:29: 5000000 INFO @ Fri, 10 Dec 2021 08:50:32: 2000000 INFO @ Fri, 10 Dec 2021 08:50:37: 11000000 INFO @ Fri, 10 Dec 2021 08:50:38: 6000000 INFO @ Fri, 10 Dec 2021 08:50:42: 3000000 INFO @ Fri, 10 Dec 2021 08:50:45: 12000000 INFO @ Fri, 10 Dec 2021 08:50:48: 7000000 INFO @ Fri, 10 Dec 2021 08:50:48: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 08:50:48: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 08:50:48: #1 total tags in treatment: 4720352 INFO @ Fri, 10 Dec 2021 08:50:48: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:50:48: #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 08:50:48: #1 tags after filtering in treatment: 4284672 INFO @ Fri, 10 Dec 2021 08:50:48: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 08:50:48: #1 finished! INFO @ Fri, 10 Dec 2021 08:50:48: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:50:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:50:49: #2 number of paired peaks: 491 WARNING @ Fri, 10 Dec 2021 08:50:49: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Fri, 10 Dec 2021 08:50:49: start model_add_line... INFO @ Fri, 10 Dec 2021 08:50:49: start X-correlation... INFO @ Fri, 10 Dec 2021 08:50:49: end of X-cor INFO @ Fri, 10 Dec 2021 08:50:49: #2 finished! INFO @ Fri, 10 Dec 2021 08:50:49: #2 predicted fragment length is 138 bps INFO @ Fri, 10 Dec 2021 08:50:49: #2 alternative fragment length(s) may be 138 bps INFO @ Fri, 10 Dec 2021 08:50:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.05_model.r WARNING @ Fri, 10 Dec 2021 08:50:49: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:50:49: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Fri, 10 Dec 2021 08:50:49: #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 08:50:49: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:50:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:50:51: 4000000 INFO @ Fri, 10 Dec 2021 08:50:57: 8000000 INFO @ Fri, 10 Dec 2021 08:50:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:51:01: 5000000 INFO @ Fri, 10 Dec 2021 08:51:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.05_peaks.xls INFO @ Fri, 10 Dec 2021 08:51:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:51:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.05_summits.bed INFO @ Fri, 10 Dec 2021 08:51:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (958 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:51:07: 9000000 INFO @ Fri, 10 Dec 2021 08:51:10: 6000000 INFO @ Fri, 10 Dec 2021 08:51:16: 10000000 INFO @ Fri, 10 Dec 2021 08:51:19: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 08:51:25: 11000000 INFO @ Fri, 10 Dec 2021 08:51:29: 8000000 INFO @ Fri, 10 Dec 2021 08:51:35: 12000000 INFO @ Fri, 10 Dec 2021 08:51:38: 9000000 INFO @ Fri, 10 Dec 2021 08:51:38: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 08:51:38: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 08:51:38: #1 total tags in treatment: 4720352 INFO @ Fri, 10 Dec 2021 08:51:38: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:51:38: #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 08:51:38: #1 tags after filtering in treatment: 4284672 INFO @ Fri, 10 Dec 2021 08:51:38: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 08:51:38: #1 finished! INFO @ Fri, 10 Dec 2021 08:51:38: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:51:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:51:38: #2 number of paired peaks: 491 WARNING @ Fri, 10 Dec 2021 08:51:38: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Fri, 10 Dec 2021 08:51:38: start model_add_line... INFO @ Fri, 10 Dec 2021 08:51:38: start X-correlation... INFO @ Fri, 10 Dec 2021 08:51:38: end of X-cor INFO @ Fri, 10 Dec 2021 08:51:38: #2 finished! INFO @ Fri, 10 Dec 2021 08:51:38: #2 predicted fragment length is 138 bps INFO @ Fri, 10 Dec 2021 08:51:38: #2 alternative fragment length(s) may be 138 bps INFO @ Fri, 10 Dec 2021 08:51:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.10_model.r WARNING @ Fri, 10 Dec 2021 08:51:38: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:51:38: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Fri, 10 Dec 2021 08:51:38: #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 08:51:38: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:51:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:51:46: 10000000 INFO @ Fri, 10 Dec 2021 08:51:48: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 08:51:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.10_peaks.xls INFO @ Fri, 10 Dec 2021 08:51:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:51:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.10_summits.bed INFO @ Fri, 10 Dec 2021 08:51:52: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (660 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:51:54: 11000000 INFO @ Fri, 10 Dec 2021 08:52:03: 12000000 INFO @ Fri, 10 Dec 2021 08:52:06: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 08:52:06: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 08:52:06: #1 total tags in treatment: 4720352 INFO @ Fri, 10 Dec 2021 08:52:06: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:52:06: #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 08:52:06: #1 tags after filtering in treatment: 4284672 INFO @ Fri, 10 Dec 2021 08:52:06: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 08:52:06: #1 finished! INFO @ Fri, 10 Dec 2021 08:52:06: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:52:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:52:06: #2 number of paired peaks: 491 WARNING @ Fri, 10 Dec 2021 08:52:06: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Fri, 10 Dec 2021 08:52:06: start model_add_line... INFO @ Fri, 10 Dec 2021 08:52:06: start X-correlation... INFO @ Fri, 10 Dec 2021 08:52:06: end of X-cor INFO @ Fri, 10 Dec 2021 08:52:06: #2 finished! INFO @ Fri, 10 Dec 2021 08:52:06: #2 predicted fragment length is 138 bps INFO @ Fri, 10 Dec 2021 08:52:06: #2 alternative fragment length(s) may be 138 bps INFO @ Fri, 10 Dec 2021 08:52:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.20_model.r WARNING @ Fri, 10 Dec 2021 08:52:06: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:52:06: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Fri, 10 Dec 2021 08:52:06: #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 08:52:06: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:52:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:52:15: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:52:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.20_peaks.xls INFO @ Fri, 10 Dec 2021 08:52:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:52:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541122/SRX7541122.20_summits.bed INFO @ Fri, 10 Dec 2021 08:52:20: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (484 records, 4 fields): 2 millis CompletedMACS2peakCalling