Job ID = 6626516 SRX = SRX5736490 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2268112 spots for SRR8956901/SRR8956901.sra Written 2268112 spots for SRR8956901/SRR8956901.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626646 ("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: 00:05:22 2268112 reads; of these: 2268112 (100.00%) were paired; of these: 305104 (13.45%) aligned concordantly 0 times 1404724 (61.93%) aligned concordantly exactly 1 time 558284 (24.61%) aligned concordantly >1 times ---- 305104 pairs aligned concordantly 0 times; of these: 136146 (44.62%) aligned discordantly 1 time ---- 168958 pairs aligned 0 times concordantly or discordantly; of these: 337916 mates make up the pairs; of these: 181565 (53.73%) aligned 0 times 63388 (18.76%) aligned exactly 1 time 92963 (27.51%) aligned >1 times 96.00% overall alignment rate Time searching: 00:05:22 Overall time: 00:05:22 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_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] 96771 / 2095565 = 0.0462 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:24:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.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 @ Tue, 14 Jul 2020 07:24:23: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:24:23: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:24:28: 1000000 INFO @ Tue, 14 Jul 2020 07:24:34: 2000000 INFO @ Tue, 14 Jul 2020 07:24:40: 3000000 INFO @ Tue, 14 Jul 2020 07:24:46: 4000000 INFO @ Tue, 14 Jul 2020 07:24:47: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:24:47: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:24:47: #1 total tags in treatment: 1875160 INFO @ Tue, 14 Jul 2020 07:24:47: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:24:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:24:47: #1 tags after filtering in treatment: 1812460 INFO @ Tue, 14 Jul 2020 07:24:47: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 14 Jul 2020 07:24:47: #1 finished! INFO @ Tue, 14 Jul 2020 07:24:47: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:24:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:24:47: #2 number of paired peaks: 512 WARNING @ Tue, 14 Jul 2020 07:24:47: Fewer paired peaks (512) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 512 pairs to build model! INFO @ Tue, 14 Jul 2020 07:24:47: start model_add_line... INFO @ Tue, 14 Jul 2020 07:24:47: start X-correlation... INFO @ Tue, 14 Jul 2020 07:24:47: end of X-cor INFO @ Tue, 14 Jul 2020 07:24:47: #2 finished! INFO @ Tue, 14 Jul 2020 07:24:47: #2 predicted fragment length is 143 bps INFO @ Tue, 14 Jul 2020 07:24:47: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 14 Jul 2020 07:24:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.05_model.r WARNING @ Tue, 14 Jul 2020 07:24:47: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:24:47: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Tue, 14 Jul 2020 07:24:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:24:47: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:24:47: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:24:51: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:24:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.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 @ Tue, 14 Jul 2020 07:24:53: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:24:53: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:24:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:24:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:24:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.05_summits.bed INFO @ Tue, 14 Jul 2020 07:24:54: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (683 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:24:59: 1000000 INFO @ Tue, 14 Jul 2020 07:25:05: 2000000 INFO @ Tue, 14 Jul 2020 07:25:12: 3000000 INFO @ Tue, 14 Jul 2020 07:25:19: 4000000 INFO @ Tue, 14 Jul 2020 07:25:20: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:25:20: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:25:20: #1 total tags in treatment: 1875160 INFO @ Tue, 14 Jul 2020 07:25:20: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:25:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:25:20: #1 tags after filtering in treatment: 1812460 INFO @ Tue, 14 Jul 2020 07:25:20: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 14 Jul 2020 07:25:20: #1 finished! INFO @ Tue, 14 Jul 2020 07:25:20: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:25:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:25:21: #2 number of paired peaks: 512 WARNING @ Tue, 14 Jul 2020 07:25:21: Fewer paired peaks (512) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 512 pairs to build model! INFO @ Tue, 14 Jul 2020 07:25:21: start model_add_line... INFO @ Tue, 14 Jul 2020 07:25:21: start X-correlation... INFO @ Tue, 14 Jul 2020 07:25:21: end of X-cor INFO @ Tue, 14 Jul 2020 07:25:21: #2 finished! INFO @ Tue, 14 Jul 2020 07:25:21: #2 predicted fragment length is 143 bps INFO @ Tue, 14 Jul 2020 07:25:21: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 14 Jul 2020 07:25:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.10_model.r WARNING @ Tue, 14 Jul 2020 07:25:21: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:25:21: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Tue, 14 Jul 2020 07:25:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:25:21: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:25:21: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:25:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.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 @ Tue, 14 Jul 2020 07:25:23: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:25:23: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:25:24: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:25:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:25:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:25:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.10_summits.bed INFO @ Tue, 14 Jul 2020 07:25:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (390 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:25:29: 1000000 INFO @ Tue, 14 Jul 2020 07:25:36: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:25:42: 3000000 INFO @ Tue, 14 Jul 2020 07:25:49: 4000000 INFO @ Tue, 14 Jul 2020 07:25:50: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:25:50: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:25:50: #1 total tags in treatment: 1875160 INFO @ Tue, 14 Jul 2020 07:25:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:25:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:25:50: #1 tags after filtering in treatment: 1812460 INFO @ Tue, 14 Jul 2020 07:25:50: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 14 Jul 2020 07:25:50: #1 finished! INFO @ Tue, 14 Jul 2020 07:25:50: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:25:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:25:50: #2 number of paired peaks: 512 WARNING @ Tue, 14 Jul 2020 07:25:50: Fewer paired peaks (512) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 512 pairs to build model! INFO @ Tue, 14 Jul 2020 07:25:50: start model_add_line... INFO @ Tue, 14 Jul 2020 07:25:51: start X-correlation... INFO @ Tue, 14 Jul 2020 07:25:51: end of X-cor INFO @ Tue, 14 Jul 2020 07:25:51: #2 finished! INFO @ Tue, 14 Jul 2020 07:25:51: #2 predicted fragment length is 143 bps INFO @ Tue, 14 Jul 2020 07:25:51: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 14 Jul 2020 07:25:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.20_model.r WARNING @ Tue, 14 Jul 2020 07:25:51: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:25:51: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Tue, 14 Jul 2020 07:25:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:25:51: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:25:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:25:54: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:25:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:25:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:25:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736490/SRX5736490.20_summits.bed INFO @ Tue, 14 Jul 2020 07:25:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (205 records, 4 fields): 12 millis CompletedMACS2peakCalling