Job ID = 8071024 SRX = SRX7917503 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T04:17:38 prefetch.2.10.7: 1) Downloading 'SRR11313084'... 2020-08-08T04:17:38 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T04:21:31 prefetch.2.10.7: HTTPS download succeed 2020-08-08T04:21:32 prefetch.2.10.7: 'SRR11313084' is valid 2020-08-08T04:21:32 prefetch.2.10.7: 1) 'SRR11313084' was downloaded successfully Read 4113682 spots for SRR11313084/SRR11313084.sra Written 4113682 spots for SRR11313084/SRR11313084.sra fastq に変換しました。 bowtie でマッピング中... Your job 8072305 ("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: 00:07:11 4113682 reads; of these: 4113682 (100.00%) were paired; of these: 1023509 (24.88%) aligned concordantly 0 times 2362292 (57.43%) aligned concordantly exactly 1 time 727881 (17.69%) aligned concordantly >1 times ---- 1023509 pairs aligned concordantly 0 times; of these: 256363 (25.05%) aligned discordantly 1 time ---- 767146 pairs aligned 0 times concordantly or discordantly; of these: 1534292 mates make up the pairs; of these: 1155580 (75.32%) aligned 0 times 178071 (11.61%) aligned exactly 1 time 200641 (13.08%) aligned >1 times 85.95% overall alignment rate Time searching: 00:07:11 Overall time: 00:07:11 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] 1169114 / 3334078 = 0.3507 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 @ Sat, 08 Aug 2020 13:30:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917503/SRX7917503.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917503/SRX7917503.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917503/SRX7917503.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917503/SRX7917503.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 @ Sat, 08 Aug 2020 13:30:58: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:30:58: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:31:05: 1000000 INFO @ Sat, 08 Aug 2020 13:31:10: 2000000 INFO @ Sat, 08 Aug 2020 13:31:17: 3000000 INFO @ Sat, 08 Aug 2020 13:31:23: 4000000 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 @ Sat, 08 Aug 2020 13:31:27: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:31:27: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:31:27: #1 total tags in treatment: 1946274 INFO @ Sat, 08 Aug 2020 13:31:27: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:31:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:31:28: #1 tags after filtering in treatment: 1465958 INFO @ Sat, 08 Aug 2020 13:31:28: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 08 Aug 2020 13:31:28: #1 finished! INFO @ Sat, 08 Aug 2020 13:31:28: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:31:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:31:28: #2 number of paired peaks: 6 WARNING @ Sat, 08 Aug 2020 13:31:28: Too few paired peaks (6) 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 @ Sat, 08 Aug 2020 13:31:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX7917503/SRX7917503.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917503/SRX7917503.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917503/SRX7917503.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917503/SRX7917503.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:31:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917503/SRX7917503.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917503/SRX7917503.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917503/SRX7917503.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917503/SRX7917503.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 @ Sat, 08 Aug 2020 13:31:28: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:31:28: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:31:34: 1000000 INFO @ Sat, 08 Aug 2020 13:31:40: 2000000 INFO @ Sat, 08 Aug 2020 13:31:46: 3000000 INFO @ Sat, 08 Aug 2020 13:31:52: 4000000 INFO @ Sat, 08 Aug 2020 13:31:56: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:31:56: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:31:56: #1 total tags in treatment: 1946274 INFO @ Sat, 08 Aug 2020 13:31:56: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:31:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:31:56: #1 tags after filtering in treatment: 1465958 INFO @ Sat, 08 Aug 2020 13:31:56: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 08 Aug 2020 13:31:56: #1 finished! INFO @ Sat, 08 Aug 2020 13:31:56: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:31:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:31:56: #2 number of paired peaks: 6 WARNING @ Sat, 08 Aug 2020 13:31:56: Too few paired peaks (6) 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 @ Sat, 08 Aug 2020 13:31:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX7917503/SRX7917503.10_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/SRX7917503/SRX7917503.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917503/SRX7917503.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917503/SRX7917503.10_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 @ Sat, 08 Aug 2020 13:31:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917503/SRX7917503.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917503/SRX7917503.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917503/SRX7917503.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917503/SRX7917503.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 @ Sat, 08 Aug 2020 13:31:59: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:31:59: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:32:05: 1000000 INFO @ Sat, 08 Aug 2020 13:32:11: 2000000 INFO @ Sat, 08 Aug 2020 13:32:16: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:32:23: 4000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:32:27: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:32:27: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:32:27: #1 total tags in treatment: 1946274 INFO @ Sat, 08 Aug 2020 13:32:27: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:32:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:32:27: #1 tags after filtering in treatment: 1465958 INFO @ Sat, 08 Aug 2020 13:32:27: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 08 Aug 2020 13:32:27: #1 finished! INFO @ Sat, 08 Aug 2020 13:32:27: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:32:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:32:27: #2 number of paired peaks: 6 WARNING @ Sat, 08 Aug 2020 13:32:27: Too few paired peaks (6) 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 @ Sat, 08 Aug 2020 13:32:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX7917503/SRX7917503.20_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/SRX7917503/SRX7917503.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917503/SRX7917503.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917503/SRX7917503.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling