Job ID = 6528241 SRX = SRX4940248 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T14:36:06 prefetch.2.10.7: 1) Downloading 'SRR8113881'... 2020-06-29T14:36:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:38:24 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:38:25 prefetch.2.10.7: 'SRR8113881' is valid 2020-06-29T14:38:25 prefetch.2.10.7: 1) 'SRR8113881' was downloaded successfully 2020-06-29T14:38:25 prefetch.2.10.7: 'SRR8113881' has 0 unresolved dependencies Read 4887355 spots for SRR8113881/SRR8113881.sra Written 4887355 spots for SRR8113881/SRR8113881.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: 00:07:47 4887355 reads; of these: 4887355 (100.00%) were paired; of these: 386252 (7.90%) aligned concordantly 0 times 3764395 (77.02%) aligned concordantly exactly 1 time 736708 (15.07%) aligned concordantly >1 times ---- 386252 pairs aligned concordantly 0 times; of these: 127110 (32.91%) aligned discordantly 1 time ---- 259142 pairs aligned 0 times concordantly or discordantly; of these: 518284 mates make up the pairs; of these: 331675 (63.99%) aligned 0 times 122638 (23.66%) aligned exactly 1 time 63971 (12.34%) aligned >1 times 96.61% overall alignment rate Time searching: 00:07:47 Overall time: 00:07:47 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] 197321 / 4575957 = 0.0431 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 23:53:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4940248/SRX4940248.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4940248/SRX4940248.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4940248/SRX4940248.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4940248/SRX4940248.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 23:53:48: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:53:48: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:53:54: 1000000 INFO @ Mon, 29 Jun 2020 23:54:00: 2000000 INFO @ Mon, 29 Jun 2020 23:54:05: 3000000 INFO @ Mon, 29 Jun 2020 23:54:10: 4000000 INFO @ Mon, 29 Jun 2020 23:54:15: 5000000 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 23:54:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4940248/SRX4940248.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4940248/SRX4940248.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4940248/SRX4940248.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4940248/SRX4940248.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 23:54:18: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:54:18: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:54:21: 6000000 INFO @ Mon, 29 Jun 2020 23:54:24: 1000000 INFO @ Mon, 29 Jun 2020 23:54:27: 7000000 INFO @ Mon, 29 Jun 2020 23:54:30: 2000000 INFO @ Mon, 29 Jun 2020 23:54:33: 8000000 INFO @ Mon, 29 Jun 2020 23:54:37: 3000000 INFO @ Mon, 29 Jun 2020 23:54:40: 9000000 INFO @ Mon, 29 Jun 2020 23:54:40: #1 tag size is determined as 75 bps INFO @ Mon, 29 Jun 2020 23:54:40: #1 tag size = 75 INFO @ Mon, 29 Jun 2020 23:54:40: #1 total tags in treatment: 4305379 INFO @ Mon, 29 Jun 2020 23:54:40: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:54:40: #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 23:54:40: #1 tags after filtering in treatment: 4160388 INFO @ Mon, 29 Jun 2020 23:54:40: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 29 Jun 2020 23:54:40: #1 finished! INFO @ Mon, 29 Jun 2020 23:54:40: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:54:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:54:40: #2 number of paired peaks: 85 WARNING @ Mon, 29 Jun 2020 23:54:40: Too few paired peaks (85) 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 23:54:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4940248/SRX4940248.05_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/SRX4940248/SRX4940248.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4940248/SRX4940248.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4940248/SRX4940248.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:54:43: 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 @ Mon, 29 Jun 2020 23:54:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4940248/SRX4940248.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4940248/SRX4940248.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4940248/SRX4940248.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4940248/SRX4940248.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 23:54:48: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:54:48: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:54:48: 5000000 INFO @ Mon, 29 Jun 2020 23:54:54: 1000000 INFO @ Mon, 29 Jun 2020 23:54:55: 6000000 INFO @ Mon, 29 Jun 2020 23:55:00: 7000000 INFO @ Mon, 29 Jun 2020 23:55:01: 2000000 INFO @ Mon, 29 Jun 2020 23:55:06: 8000000 INFO @ Mon, 29 Jun 2020 23:55:07: 3000000 INFO @ Mon, 29 Jun 2020 23:55:13: 9000000 INFO @ Mon, 29 Jun 2020 23:55:13: #1 tag size is determined as 75 bps INFO @ Mon, 29 Jun 2020 23:55:13: #1 tag size = 75 INFO @ Mon, 29 Jun 2020 23:55:13: #1 total tags in treatment: 4305379 INFO @ Mon, 29 Jun 2020 23:55:13: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:55:13: #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 23:55:13: #1 tags after filtering in treatment: 4160388 INFO @ Mon, 29 Jun 2020 23:55:13: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 29 Jun 2020 23:55:13: #1 finished! INFO @ Mon, 29 Jun 2020 23:55:13: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:55:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:55:13: #2 number of paired peaks: 85 WARNING @ Mon, 29 Jun 2020 23:55:13: Too few paired peaks (85) 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 23:55:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4940248/SRX4940248.10_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/SRX4940248/SRX4940248.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4940248/SRX4940248.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4940248/SRX4940248.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:55:14: 4000000 INFO @ Mon, 29 Jun 2020 23:55:20: 5000000 INFO @ Mon, 29 Jun 2020 23:55:26: 6000000 INFO @ Mon, 29 Jun 2020 23:55:31: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:55:37: 8000000 INFO @ Mon, 29 Jun 2020 23:55:42: 9000000 INFO @ Mon, 29 Jun 2020 23:55:43: #1 tag size is determined as 75 bps INFO @ Mon, 29 Jun 2020 23:55:43: #1 tag size = 75 INFO @ Mon, 29 Jun 2020 23:55:43: #1 total tags in treatment: 4305379 INFO @ Mon, 29 Jun 2020 23:55:43: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:55:43: #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 23:55:43: #1 tags after filtering in treatment: 4160388 INFO @ Mon, 29 Jun 2020 23:55:43: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 29 Jun 2020 23:55:43: #1 finished! INFO @ Mon, 29 Jun 2020 23:55:43: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:55:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:55:43: #2 number of paired peaks: 85 WARNING @ Mon, 29 Jun 2020 23:55:43: Too few paired peaks (85) 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 23:55:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4940248/SRX4940248.20_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/SRX4940248/SRX4940248.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4940248/SRX4940248.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4940248/SRX4940248.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。