Job ID = 6527980 SRX = SRX3632894 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T14:13:50 prefetch.2.10.7: 1) Downloading 'SRR6655528'... 2020-06-29T14:13:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:15:11 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:15:12 prefetch.2.10.7: 'SRR6655528' is valid 2020-06-29T14:15:12 prefetch.2.10.7: 1) 'SRR6655528' was downloaded successfully 2020-06-29T14:15:12 prefetch.2.10.7: 'SRR6655528' has 0 unresolved dependencies Read 7354316 spots for SRR6655528/SRR6655528.sra Written 7354316 spots for SRR6655528/SRR6655528.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: 00:13:57 7354316 reads; of these: 7354316 (100.00%) were paired; of these: 601493 (8.18%) aligned concordantly 0 times 5352647 (72.78%) aligned concordantly exactly 1 time 1400176 (19.04%) aligned concordantly >1 times ---- 601493 pairs aligned concordantly 0 times; of these: 174153 (28.95%) aligned discordantly 1 time ---- 427340 pairs aligned 0 times concordantly or discordantly; of these: 854680 mates make up the pairs; of these: 517688 (60.57%) aligned 0 times 224134 (26.22%) aligned exactly 1 time 112858 (13.20%) aligned >1 times 96.48% overall alignment rate Time searching: 00:13:57 Overall time: 00:13:57 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_sort_core] merging from 8 files... [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] 260083 / 6419746 = 0.0405 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 23:37:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3632894/SRX3632894.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3632894/SRX3632894.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3632894/SRX3632894.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3632894/SRX3632894.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 23:37:59: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:37:59: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:38:04: 1000000 INFO @ Mon, 29 Jun 2020 23:38:10: 2000000 INFO @ Mon, 29 Jun 2020 23:38:15: 3000000 INFO @ Mon, 29 Jun 2020 23:38:20: 4000000 INFO @ Mon, 29 Jun 2020 23:38:26: 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 23:38:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3632894/SRX3632894.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3632894/SRX3632894.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3632894/SRX3632894.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3632894/SRX3632894.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 23:38:29: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:38:29: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:38:31: 6000000 INFO @ Mon, 29 Jun 2020 23:38:35: 1000000 INFO @ Mon, 29 Jun 2020 23:38:37: 7000000 INFO @ Mon, 29 Jun 2020 23:38:40: 2000000 INFO @ Mon, 29 Jun 2020 23:38:43: 8000000 INFO @ Mon, 29 Jun 2020 23:38:46: 3000000 INFO @ Mon, 29 Jun 2020 23:38:48: 9000000 INFO @ Mon, 29 Jun 2020 23:38:51: 4000000 INFO @ Mon, 29 Jun 2020 23:38:54: 10000000 INFO @ Mon, 29 Jun 2020 23:38:57: 5000000 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 23:38:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3632894/SRX3632894.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3632894/SRX3632894.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3632894/SRX3632894.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3632894/SRX3632894.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 23:38:59: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:38:59: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:38:59: 11000000 INFO @ Mon, 29 Jun 2020 23:39:03: 6000000 INFO @ Mon, 29 Jun 2020 23:39:05: 1000000 INFO @ Mon, 29 Jun 2020 23:39:05: 12000000 INFO @ Mon, 29 Jun 2020 23:39:09: 7000000 INFO @ Mon, 29 Jun 2020 23:39:11: 2000000 INFO @ Mon, 29 Jun 2020 23:39:11: 13000000 INFO @ Mon, 29 Jun 2020 23:39:14: 8000000 INFO @ Mon, 29 Jun 2020 23:39:15: #1 tag size is determined as 74 bps INFO @ Mon, 29 Jun 2020 23:39:15: #1 tag size = 74 INFO @ Mon, 29 Jun 2020 23:39:15: #1 total tags in treatment: 6499234 INFO @ Mon, 29 Jun 2020 23:39:15: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:39:15: #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 23:39:15: #1 tags after filtering in treatment: 6125897 INFO @ Mon, 29 Jun 2020 23:39:15: #1 Redundant rate of treatment: 0.06 INFO @ Mon, 29 Jun 2020 23:39:15: #1 finished! INFO @ Mon, 29 Jun 2020 23:39:15: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:39:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:39:16: #2 number of paired peaks: 47 WARNING @ Mon, 29 Jun 2020 23:39:16: Too few paired peaks (47) 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 23:39:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3632894/SRX3632894.05_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/SRX3632894/SRX3632894.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632894/SRX3632894.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632894/SRX3632894.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:39:16: 3000000 INFO @ Mon, 29 Jun 2020 23:39:20: 9000000 INFO @ Mon, 29 Jun 2020 23:39:22: 4000000 INFO @ Mon, 29 Jun 2020 23:39:26: 10000000 INFO @ Mon, 29 Jun 2020 23:39:28: 5000000 INFO @ Mon, 29 Jun 2020 23:39:32: 11000000 INFO @ Mon, 29 Jun 2020 23:39:34: 6000000 INFO @ Mon, 29 Jun 2020 23:39:37: 12000000 INFO @ Mon, 29 Jun 2020 23:39:40: 7000000 INFO @ Mon, 29 Jun 2020 23:39:43: 13000000 INFO @ Mon, 29 Jun 2020 23:39:45: 8000000 INFO @ Mon, 29 Jun 2020 23:39:47: #1 tag size is determined as 74 bps INFO @ Mon, 29 Jun 2020 23:39:47: #1 tag size = 74 INFO @ Mon, 29 Jun 2020 23:39:47: #1 total tags in treatment: 6499234 INFO @ Mon, 29 Jun 2020 23:39:47: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:39:47: #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 23:39:47: #1 tags after filtering in treatment: 6125897 INFO @ Mon, 29 Jun 2020 23:39:47: #1 Redundant rate of treatment: 0.06 INFO @ Mon, 29 Jun 2020 23:39:47: #1 finished! INFO @ Mon, 29 Jun 2020 23:39:47: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:39:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:39:48: #2 number of paired peaks: 47 WARNING @ Mon, 29 Jun 2020 23:39:48: Too few paired peaks (47) 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 23:39:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3632894/SRX3632894.10_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/SRX3632894/SRX3632894.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632894/SRX3632894.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632894/SRX3632894.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:39:51: 9000000 INFO @ Mon, 29 Jun 2020 23:39:57: 10000000 INFO @ Mon, 29 Jun 2020 23:40:02: 11000000 INFO @ Mon, 29 Jun 2020 23:40:08: 12000000 INFO @ Mon, 29 Jun 2020 23:40:14: 13000000 INFO @ Mon, 29 Jun 2020 23:40:17: #1 tag size is determined as 74 bps INFO @ Mon, 29 Jun 2020 23:40:17: #1 tag size = 74 INFO @ Mon, 29 Jun 2020 23:40:17: #1 total tags in treatment: 6499234 INFO @ Mon, 29 Jun 2020 23:40:17: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:40:17: #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 23:40:17: #1 tags after filtering in treatment: 6125897 INFO @ Mon, 29 Jun 2020 23:40:17: #1 Redundant rate of treatment: 0.06 INFO @ Mon, 29 Jun 2020 23:40:17: #1 finished! INFO @ Mon, 29 Jun 2020 23:40:17: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:40:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:40:18: #2 number of paired peaks: 47 WARNING @ Mon, 29 Jun 2020 23:40:18: Too few paired peaks (47) 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 23:40:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3632894/SRX3632894.20_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/SRX3632894/SRX3632894.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632894/SRX3632894.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632894/SRX3632894.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。