Job ID = 8069686 SRX = SRX7917421 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:45:12 prefetch.2.10.7: 1) Downloading 'SRR11313002'... 2020-08-08T03:45:12 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:45:42 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:45:42 prefetch.2.10.7: 'SRR11313002' is valid 2020-08-08T03:45:42 prefetch.2.10.7: 1) 'SRR11313002' was downloaded successfully Read 3623320 spots for SRR11313002/SRR11313002.sra Written 3623320 spots for SRR11313002/SRR11313002.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070552 ("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: 00:07:14 3623320 reads; of these: 3623320 (100.00%) were paired; of these: 780061 (21.53%) aligned concordantly 0 times 2112042 (58.29%) aligned concordantly exactly 1 time 731217 (20.18%) aligned concordantly >1 times ---- 780061 pairs aligned concordantly 0 times; of these: 360019 (46.15%) aligned discordantly 1 time ---- 420042 pairs aligned 0 times concordantly or discordantly; of these: 840084 mates make up the pairs; of these: 306203 (36.45%) aligned 0 times 211357 (25.16%) aligned exactly 1 time 322524 (38.39%) aligned >1 times 95.77% overall alignment rate Time searching: 00:07:14 Overall time: 00:07:14 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] 1065150 / 3191928 = 0.3337 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 12:55:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917421/SRX7917421.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917421/SRX7917421.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917421/SRX7917421.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917421/SRX7917421.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 12:55:11: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:55:11: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:55:15: 1000000 INFO @ Sat, 08 Aug 2020 12:55:20: 2000000 INFO @ Sat, 08 Aug 2020 12:55:25: 3000000 INFO @ Sat, 08 Aug 2020 12:55:29: 4000000 INFO @ Sat, 08 Aug 2020 12:55:33: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:55:33: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:55:33: #1 total tags in treatment: 1836394 INFO @ Sat, 08 Aug 2020 12:55:33: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:55:33: #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 12:55:33: #1 tags after filtering in treatment: 1397466 INFO @ Sat, 08 Aug 2020 12:55:33: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 08 Aug 2020 12:55:33: #1 finished! INFO @ Sat, 08 Aug 2020 12:55:33: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:55:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:55:33: #2 number of paired peaks: 2 WARNING @ Sat, 08 Aug 2020 12:55:33: Too few paired peaks (2) 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 12:55:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX7917421/SRX7917421.05_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/SRX7917421/SRX7917421.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917421/SRX7917421.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917421/SRX7917421.05_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 @ Sat, 08 Aug 2020 12:55:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917421/SRX7917421.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917421/SRX7917421.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917421/SRX7917421.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917421/SRX7917421.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 12:55:41: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:55:41: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:55:45: 1000000 INFO @ Sat, 08 Aug 2020 12:55:50: 2000000 INFO @ Sat, 08 Aug 2020 12:55:55: 3000000 INFO @ Sat, 08 Aug 2020 12:55:59: 4000000 INFO @ Sat, 08 Aug 2020 12:56:03: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:56:03: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:56:03: #1 total tags in treatment: 1836394 INFO @ Sat, 08 Aug 2020 12:56:03: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:56:03: #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 12:56:03: #1 tags after filtering in treatment: 1397466 INFO @ Sat, 08 Aug 2020 12:56:03: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 08 Aug 2020 12:56:03: #1 finished! INFO @ Sat, 08 Aug 2020 12:56:03: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:56:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:56:03: #2 number of paired peaks: 2 WARNING @ Sat, 08 Aug 2020 12:56:03: Too few paired peaks (2) 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 12:56:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX7917421/SRX7917421.10_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/SRX7917421/SRX7917421.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917421/SRX7917421.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917421/SRX7917421.10_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 12:56:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917421/SRX7917421.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917421/SRX7917421.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917421/SRX7917421.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917421/SRX7917421.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 12:56:11: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:56:11: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:56:15: 1000000 INFO @ Sat, 08 Aug 2020 12:56:20: 2000000 INFO @ Sat, 08 Aug 2020 12:56:25: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:56:29: 4000000 INFO @ Sat, 08 Aug 2020 12:56:34: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:56:34: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:56:34: #1 total tags in treatment: 1836394 INFO @ Sat, 08 Aug 2020 12:56:34: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:56:34: #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 12:56:34: #1 tags after filtering in treatment: 1397466 INFO @ Sat, 08 Aug 2020 12:56:34: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 08 Aug 2020 12:56:34: #1 finished! INFO @ Sat, 08 Aug 2020 12:56:34: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:56:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:56:34: #2 number of paired peaks: 2 WARNING @ Sat, 08 Aug 2020 12:56:34: Too few paired peaks (2) 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 12:56:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX7917421/SRX7917421.20_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/SRX7917421/SRX7917421.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917421/SRX7917421.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917421/SRX7917421.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。