Job ID = 6527957 SRX = SRX3434308 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T14:11:35 prefetch.2.10.7: 1) Downloading 'SRR6335190'... 2020-06-29T14:11:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:12:09 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:12:09 prefetch.2.10.7: 'SRR6335190' is valid 2020-06-29T14:12:09 prefetch.2.10.7: 1) 'SRR6335190' was downloaded successfully 2020-06-29T14:12:09 prefetch.2.10.7: 'SRR6335190' has 0 unresolved dependencies Read 794239 spots for SRR6335190/SRR6335190.sra Written 794239 spots for SRR6335190/SRR6335190.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: 00:00:50 794239 reads; of these: 794239 (100.00%) were paired; of these: 150255 (18.92%) aligned concordantly 0 times 580184 (73.05%) aligned concordantly exactly 1 time 63800 (8.03%) aligned concordantly >1 times ---- 150255 pairs aligned concordantly 0 times; of these: 53015 (35.28%) aligned discordantly 1 time ---- 97240 pairs aligned 0 times concordantly or discordantly; of these: 194480 mates make up the pairs; of these: 149227 (76.73%) aligned 0 times 31341 (16.12%) aligned exactly 1 time 13912 (7.15%) aligned >1 times 90.61% overall alignment rate Time searching: 00:00:50 Overall time: 00:00:50 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] 9712 / 550132 = 0.0177 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 @ Mon, 29 Jun 2020 23:14:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.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 @ Mon, 29 Jun 2020 23:14:36: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:14:36: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:14:44: 1000000 INFO @ Mon, 29 Jun 2020 23:14:47: #1 tag size is determined as 73 bps INFO @ Mon, 29 Jun 2020 23:14:47: #1 tag size = 73 INFO @ Mon, 29 Jun 2020 23:14:47: #1 total tags in treatment: 634785 INFO @ Mon, 29 Jun 2020 23:14:47: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:14:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:14:47: #1 tags after filtering in treatment: 628197 INFO @ Mon, 29 Jun 2020 23:14:47: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 29 Jun 2020 23:14:47: #1 finished! INFO @ Mon, 29 Jun 2020 23:14:47: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:14:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:14:47: #2 number of paired peaks: 47 WARNING @ Mon, 29 Jun 2020 23:14:47: Too few paired peaks (47) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Mon, 29 Jun 2020 23:14:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 @ Mon, 29 Jun 2020 23:15:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.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 @ Mon, 29 Jun 2020 23:15:06: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:15:06: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:15:12: 1000000 INFO @ Mon, 29 Jun 2020 23:15:15: #1 tag size is determined as 73 bps INFO @ Mon, 29 Jun 2020 23:15:15: #1 tag size = 73 INFO @ Mon, 29 Jun 2020 23:15:15: #1 total tags in treatment: 634785 INFO @ Mon, 29 Jun 2020 23:15:15: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:15:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:15:15: #1 tags after filtering in treatment: 628197 INFO @ Mon, 29 Jun 2020 23:15:15: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 29 Jun 2020 23:15:15: #1 finished! INFO @ Mon, 29 Jun 2020 23:15:15: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:15:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:15:15: #2 number of paired peaks: 47 WARNING @ Mon, 29 Jun 2020 23:15:15: Too few paired peaks (47) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Mon, 29 Jun 2020 23:15:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 @ Mon, 29 Jun 2020 23:15:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.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 @ Mon, 29 Jun 2020 23:15:36: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:15:36: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:15:44: 1000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:15:48: #1 tag size is determined as 73 bps INFO @ Mon, 29 Jun 2020 23:15:48: #1 tag size = 73 INFO @ Mon, 29 Jun 2020 23:15:48: #1 total tags in treatment: 634785 INFO @ Mon, 29 Jun 2020 23:15:48: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:15:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:15:48: #1 tags after filtering in treatment: 628197 INFO @ Mon, 29 Jun 2020 23:15:48: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 29 Jun 2020 23:15:48: #1 finished! INFO @ Mon, 29 Jun 2020 23:15:48: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:15:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:15:48: #2 number of paired peaks: 47 WARNING @ Mon, 29 Jun 2020 23:15:48: Too few paired peaks (47) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Mon, 29 Jun 2020 23:15:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3434308/SRX3434308.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling