Job ID = 6527979 SRX = SRX3632893 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T13:51:48 prefetch.2.10.7: 1) Downloading 'SRR6655527'... 2020-06-29T13:51:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:52:36 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:52:36 prefetch.2.10.7: 'SRR6655527' is valid 2020-06-29T13:52:36 prefetch.2.10.7: 1) 'SRR6655527' was downloaded successfully 2020-06-29T13:52:36 prefetch.2.10.7: 'SRR6655527' has 0 unresolved dependencies Read 2907031 spots for SRR6655527/SRR6655527.sra Written 2907031 spots for SRR6655527/SRR6655527.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: 00:05:00 2907031 reads; of these: 2907031 (100.00%) were paired; of these: 350427 (12.05%) aligned concordantly 0 times 2099071 (72.21%) aligned concordantly exactly 1 time 457533 (15.74%) aligned concordantly >1 times ---- 350427 pairs aligned concordantly 0 times; of these: 67883 (19.37%) aligned discordantly 1 time ---- 282544 pairs aligned 0 times concordantly or discordantly; of these: 565088 mates make up the pairs; of these: 428285 (75.79%) aligned 0 times 90958 (16.10%) aligned exactly 1 time 45845 (8.11%) aligned >1 times 92.63% overall alignment rate Time searching: 00:05:00 Overall time: 00:05:00 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] 132835 / 2593213 = 0.0512 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 23:01:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3632893/SRX3632893.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3632893/SRX3632893.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3632893/SRX3632893.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3632893/SRX3632893.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 23:01:30: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:01:30: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:01:37: 1000000 INFO @ Mon, 29 Jun 2020 23:01:44: 2000000 INFO @ Mon, 29 Jun 2020 23:01:51: 3000000 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 23:01:59: 4000000 INFO @ Mon, 29 Jun 2020 23:02:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3632893/SRX3632893.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3632893/SRX3632893.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3632893/SRX3632893.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3632893/SRX3632893.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 23:02:00: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:02:00: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:02:06: 5000000 INFO @ Mon, 29 Jun 2020 23:02:07: 1000000 INFO @ Mon, 29 Jun 2020 23:02:07: #1 tag size is determined as 75 bps INFO @ Mon, 29 Jun 2020 23:02:07: #1 tag size = 75 INFO @ Mon, 29 Jun 2020 23:02:07: #1 total tags in treatment: 2429217 INFO @ Mon, 29 Jun 2020 23:02:07: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:02:07: #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 23:02:07: #1 tags after filtering in treatment: 2364476 INFO @ Mon, 29 Jun 2020 23:02:07: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 29 Jun 2020 23:02:07: #1 finished! INFO @ Mon, 29 Jun 2020 23:02:07: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:02:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:02:07: #2 number of paired peaks: 88 WARNING @ Mon, 29 Jun 2020 23:02:07: Too few paired peaks (88) 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 23:02:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3632893/SRX3632893.05_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/SRX3632893/SRX3632893.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632893/SRX3632893.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632893/SRX3632893.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:02:14: 2000000 INFO @ Mon, 29 Jun 2020 23:02:22: 3000000 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 23:02:29: 4000000 INFO @ Mon, 29 Jun 2020 23:02:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3632893/SRX3632893.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3632893/SRX3632893.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3632893/SRX3632893.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3632893/SRX3632893.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 23:02:30: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:02:30: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:02:37: 5000000 INFO @ Mon, 29 Jun 2020 23:02:37: 1000000 INFO @ Mon, 29 Jun 2020 23:02:37: #1 tag size is determined as 75 bps INFO @ Mon, 29 Jun 2020 23:02:37: #1 tag size = 75 INFO @ Mon, 29 Jun 2020 23:02:37: #1 total tags in treatment: 2429217 INFO @ Mon, 29 Jun 2020 23:02:37: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:02:37: #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 23:02:38: #1 tags after filtering in treatment: 2364476 INFO @ Mon, 29 Jun 2020 23:02:38: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 29 Jun 2020 23:02:38: #1 finished! INFO @ Mon, 29 Jun 2020 23:02:38: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:02:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:02:38: #2 number of paired peaks: 88 WARNING @ Mon, 29 Jun 2020 23:02:38: Too few paired peaks (88) 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 23:02:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3632893/SRX3632893.10_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/SRX3632893/SRX3632893.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632893/SRX3632893.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632893/SRX3632893.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:02:44: 2000000 INFO @ Mon, 29 Jun 2020 23:02:50: 3000000 INFO @ Mon, 29 Jun 2020 23:02:57: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:03:03: 5000000 INFO @ Mon, 29 Jun 2020 23:03:04: #1 tag size is determined as 75 bps INFO @ Mon, 29 Jun 2020 23:03:04: #1 tag size = 75 INFO @ Mon, 29 Jun 2020 23:03:04: #1 total tags in treatment: 2429217 INFO @ Mon, 29 Jun 2020 23:03:04: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:03:04: #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 23:03:04: #1 tags after filtering in treatment: 2364476 INFO @ Mon, 29 Jun 2020 23:03:04: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 29 Jun 2020 23:03:04: #1 finished! INFO @ Mon, 29 Jun 2020 23:03:04: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:03:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:03:04: #2 number of paired peaks: 88 WARNING @ Mon, 29 Jun 2020 23:03:04: Too few paired peaks (88) 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 23:03:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3632893/SRX3632893.20_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/SRX3632893/SRX3632893.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632893/SRX3632893.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632893/SRX3632893.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。