Job ID = 8069721 SRX = SRX7917431 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:47:42 prefetch.2.10.7: 1) Downloading 'SRR11313012'... 2020-08-08T03:47:42 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:48:30 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:48:30 prefetch.2.10.7: 'SRR11313012' is valid 2020-08-08T03:48:30 prefetch.2.10.7: 1) 'SRR11313012' was downloaded successfully Read 3621251 spots for SRR11313012/SRR11313012.sra Written 3621251 spots for SRR11313012/SRR11313012.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070668 ("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: 00:06:51 3621251 reads; of these: 3621251 (100.00%) were paired; of these: 663946 (18.33%) aligned concordantly 0 times 2265004 (62.55%) aligned concordantly exactly 1 time 692301 (19.12%) aligned concordantly >1 times ---- 663946 pairs aligned concordantly 0 times; of these: 253533 (38.19%) aligned discordantly 1 time ---- 410413 pairs aligned 0 times concordantly or discordantly; of these: 820826 mates make up the pairs; of these: 443873 (54.08%) aligned 0 times 178525 (21.75%) aligned exactly 1 time 198428 (24.17%) aligned >1 times 93.87% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 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] 1074642 / 3198768 = 0.3360 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 12:57:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917431/SRX7917431.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917431/SRX7917431.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917431/SRX7917431.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917431/SRX7917431.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 12:57:31: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:57:31: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:57:38: 1000000 INFO @ Sat, 08 Aug 2020 12:57:44: 2000000 INFO @ Sat, 08 Aug 2020 12:57:51: 3000000 INFO @ Sat, 08 Aug 2020 12:57:57: 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 12:58:01: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:58:01: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:58:01: #1 total tags in treatment: 1907243 INFO @ Sat, 08 Aug 2020 12:58:01: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:01: #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 12:58:01: #1 tags after filtering in treatment: 1466653 INFO @ Sat, 08 Aug 2020 12:58:01: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 08 Aug 2020 12:58:01: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:01: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:01: #2 number of paired peaks: 13 WARNING @ Sat, 08 Aug 2020 12:58:01: Too few paired peaks (13) 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 12:58:01: Process for pairing-model is terminated! INFO @ Sat, 08 Aug 2020 12:58:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917431/SRX7917431.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917431/SRX7917431.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917431/SRX7917431.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917431/SRX7917431.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 12:58:01: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:58:01: #1 read treatment tags... cut: /home/okishinya/chipatlas/results/dm3/SRX7917431/SRX7917431.05_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/SRX7917431/SRX7917431.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917431/SRX7917431.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917431/SRX7917431.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:58:08: 1000000 INFO @ Sat, 08 Aug 2020 12:58:15: 2000000 INFO @ Sat, 08 Aug 2020 12:58:21: 3000000 INFO @ Sat, 08 Aug 2020 12:58:28: 4000000 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 12:58:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917431/SRX7917431.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917431/SRX7917431.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917431/SRX7917431.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917431/SRX7917431.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 12:58:31: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:58:31: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:58:32: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:58:32: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:58:32: #1 total tags in treatment: 1907243 INFO @ Sat, 08 Aug 2020 12:58:32: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:32: #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 12:58:32: #1 tags after filtering in treatment: 1466653 INFO @ Sat, 08 Aug 2020 12:58:32: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 08 Aug 2020 12:58:32: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:32: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:32: #2 number of paired peaks: 13 WARNING @ Sat, 08 Aug 2020 12:58:32: Too few paired peaks (13) 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 12:58:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX7917431/SRX7917431.10_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/SRX7917431/SRX7917431.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917431/SRX7917431.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917431/SRX7917431.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:58:38: 1000000 INFO @ Sat, 08 Aug 2020 12:58:44: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:58:50: 3000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:58:57: 4000000 INFO @ Sat, 08 Aug 2020 12:59:01: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:59:01: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:59:01: #1 total tags in treatment: 1907243 INFO @ Sat, 08 Aug 2020 12:59:01: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:59:01: #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 12:59:01: #1 tags after filtering in treatment: 1466653 INFO @ Sat, 08 Aug 2020 12:59:01: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 08 Aug 2020 12:59:01: #1 finished! INFO @ Sat, 08 Aug 2020 12:59:01: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:59:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:59:01: #2 number of paired peaks: 13 WARNING @ Sat, 08 Aug 2020 12:59:01: Too few paired peaks (13) 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 12:59:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX7917431/SRX7917431.20_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/SRX7917431/SRX7917431.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917431/SRX7917431.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917431/SRX7917431.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling