Job ID = 6528142 SRX = SRX474606 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T14:38:21 prefetch.2.10.7: 1) Downloading 'SRR1174459'... 2020-06-29T14:38:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:48:09 prefetch.2.10.7: HTTPS download failed 2020-06-29T14:48:09 prefetch.2.10.7: 1) failed to download SRR1174459 2020-06-29T14:48:23 prefetch.2.10.7: 1) Downloading 'SRR1174459'... 2020-06-29T14:48:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:48:23 prefetch.2.10.7: Continue download of 'SRR1174459' from 1003372756 2020-06-29T14:48:31 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:48:31 prefetch.2.10.7: 1) 'SRR1174459' was downloaded successfully 2020-06-29T14:48:31 prefetch.2.10.7: 'SRR1174459' has 0 unresolved dependencies Read 16150832 spots for SRR1174459/SRR1174459.sra Written 16150832 spots for SRR1174459/SRR1174459.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: 00:42:01 16150832 reads; of these: 16150832 (100.00%) were paired; of these: 823836 (5.10%) aligned concordantly 0 times 11034008 (68.32%) aligned concordantly exactly 1 time 4292988 (26.58%) aligned concordantly >1 times ---- 823836 pairs aligned concordantly 0 times; of these: 92874 (11.27%) aligned discordantly 1 time ---- 730962 pairs aligned 0 times concordantly or discordantly; of these: 1461924 mates make up the pairs; of these: 1027960 (70.32%) aligned 0 times 287037 (19.63%) aligned exactly 1 time 146927 (10.05%) aligned >1 times 96.82% overall alignment rate Time searching: 00:42:01 Overall time: 00:42:01 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 16 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] 875417 / 15380810 = 0.0569 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 @ Tue, 30 Jun 2020 00:53:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474606/SRX474606.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474606/SRX474606.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474606/SRX474606.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474606/SRX474606.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 @ Tue, 30 Jun 2020 00:53:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:53:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:53:58: 1000000 INFO @ Tue, 30 Jun 2020 00:54:05: 2000000 INFO @ Tue, 30 Jun 2020 00:54:12: 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 @ Tue, 30 Jun 2020 00:54:18: 4000000 INFO @ Tue, 30 Jun 2020 00:54:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474606/SRX474606.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474606/SRX474606.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474606/SRX474606.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474606/SRX474606.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 @ Tue, 30 Jun 2020 00:54:19: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:54:19: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:54:25: 5000000 INFO @ Tue, 30 Jun 2020 00:54:26: 1000000 INFO @ Tue, 30 Jun 2020 00:54:32: 6000000 INFO @ Tue, 30 Jun 2020 00:54:33: 2000000 INFO @ Tue, 30 Jun 2020 00:54:39: 7000000 INFO @ Tue, 30 Jun 2020 00:54:40: 3000000 INFO @ Tue, 30 Jun 2020 00:54:46: 8000000 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 @ Tue, 30 Jun 2020 00:54:47: 4000000 INFO @ Tue, 30 Jun 2020 00:54:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474606/SRX474606.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474606/SRX474606.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474606/SRX474606.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474606/SRX474606.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 @ Tue, 30 Jun 2020 00:54:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:54:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:54:53: 9000000 INFO @ Tue, 30 Jun 2020 00:54:55: 5000000 INFO @ Tue, 30 Jun 2020 00:54:57: 1000000 INFO @ Tue, 30 Jun 2020 00:55:00: 10000000 INFO @ Tue, 30 Jun 2020 00:55:02: 6000000 INFO @ Tue, 30 Jun 2020 00:55:04: 2000000 INFO @ Tue, 30 Jun 2020 00:55:07: 11000000 INFO @ Tue, 30 Jun 2020 00:55:10: 7000000 INFO @ Tue, 30 Jun 2020 00:55:12: 3000000 INFO @ Tue, 30 Jun 2020 00:55:14: 12000000 INFO @ Tue, 30 Jun 2020 00:55:17: 8000000 INFO @ Tue, 30 Jun 2020 00:55:19: 4000000 INFO @ Tue, 30 Jun 2020 00:55:21: 13000000 INFO @ Tue, 30 Jun 2020 00:55:25: 9000000 INFO @ Tue, 30 Jun 2020 00:55:27: 5000000 INFO @ Tue, 30 Jun 2020 00:55:27: 14000000 INFO @ Tue, 30 Jun 2020 00:55:32: 10000000 INFO @ Tue, 30 Jun 2020 00:55:34: 6000000 INFO @ Tue, 30 Jun 2020 00:55:34: 15000000 INFO @ Tue, 30 Jun 2020 00:55:40: 11000000 INFO @ Tue, 30 Jun 2020 00:55:41: 16000000 INFO @ Tue, 30 Jun 2020 00:55:42: 7000000 INFO @ Tue, 30 Jun 2020 00:55:48: 17000000 INFO @ Tue, 30 Jun 2020 00:55:49: 12000000 INFO @ Tue, 30 Jun 2020 00:55:50: 8000000 INFO @ Tue, 30 Jun 2020 00:55:56: 18000000 INFO @ Tue, 30 Jun 2020 00:55:57: 13000000 INFO @ Tue, 30 Jun 2020 00:55:58: 9000000 INFO @ Tue, 30 Jun 2020 00:56:03: 19000000 INFO @ Tue, 30 Jun 2020 00:56:04: 14000000 INFO @ Tue, 30 Jun 2020 00:56:06: 10000000 INFO @ Tue, 30 Jun 2020 00:56:10: 20000000 INFO @ Tue, 30 Jun 2020 00:56:12: 15000000 INFO @ Tue, 30 Jun 2020 00:56:14: 11000000 INFO @ Tue, 30 Jun 2020 00:56:17: 21000000 INFO @ Tue, 30 Jun 2020 00:56:21: 16000000 INFO @ Tue, 30 Jun 2020 00:56:22: 12000000 INFO @ Tue, 30 Jun 2020 00:56:24: 22000000 INFO @ Tue, 30 Jun 2020 00:56:29: 17000000 INFO @ Tue, 30 Jun 2020 00:56:30: 13000000 INFO @ Tue, 30 Jun 2020 00:56:31: 23000000 INFO @ Tue, 30 Jun 2020 00:56:36: 18000000 INFO @ Tue, 30 Jun 2020 00:56:38: 14000000 INFO @ Tue, 30 Jun 2020 00:56:38: 24000000 INFO @ Tue, 30 Jun 2020 00:56:45: 19000000 INFO @ Tue, 30 Jun 2020 00:56:46: 25000000 INFO @ Tue, 30 Jun 2020 00:56:46: 15000000 INFO @ Tue, 30 Jun 2020 00:56:53: 26000000 INFO @ Tue, 30 Jun 2020 00:56:53: 20000000 INFO @ Tue, 30 Jun 2020 00:56:55: 16000000 INFO @ Tue, 30 Jun 2020 00:57:00: 27000000 INFO @ Tue, 30 Jun 2020 00:57:02: 21000000 INFO @ Tue, 30 Jun 2020 00:57:03: 17000000 INFO @ Tue, 30 Jun 2020 00:57:07: 28000000 INFO @ Tue, 30 Jun 2020 00:57:09: 22000000 INFO @ Tue, 30 Jun 2020 00:57:11: 18000000 INFO @ Tue, 30 Jun 2020 00:57:14: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:57:17: 23000000 INFO @ Tue, 30 Jun 2020 00:57:18: 19000000 INFO @ Tue, 30 Jun 2020 00:57:19: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:57:19: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:57:19: #1 total tags in treatment: 14452710 INFO @ Tue, 30 Jun 2020 00:57:19: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:57:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:57:19: #1 tags after filtering in treatment: 12561473 INFO @ Tue, 30 Jun 2020 00:57:19: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 30 Jun 2020 00:57:19: #1 finished! INFO @ Tue, 30 Jun 2020 00:57:19: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:57:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:57:20: #2 number of paired peaks: 71 WARNING @ Tue, 30 Jun 2020 00:57:20: Too few paired peaks (71) 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 @ Tue, 30 Jun 2020 00:57:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474606/SRX474606.05_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/SRX474606/SRX474606.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474606/SRX474606.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474606/SRX474606.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:57:25: 24000000 INFO @ Tue, 30 Jun 2020 00:57:26: 20000000 INFO @ Tue, 30 Jun 2020 00:57:32: 25000000 INFO @ Tue, 30 Jun 2020 00:57:33: 21000000 INFO @ Tue, 30 Jun 2020 00:57:39: 26000000 INFO @ Tue, 30 Jun 2020 00:57:40: 22000000 INFO @ Tue, 30 Jun 2020 00:57:46: 27000000 INFO @ Tue, 30 Jun 2020 00:57:48: 23000000 INFO @ Tue, 30 Jun 2020 00:57:54: 28000000 INFO @ Tue, 30 Jun 2020 00:57:55: 24000000 INFO @ Tue, 30 Jun 2020 00:58:01: 29000000 INFO @ Tue, 30 Jun 2020 00:58:02: 25000000 INFO @ Tue, 30 Jun 2020 00:58:05: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:58:05: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:58:05: #1 total tags in treatment: 14452710 INFO @ Tue, 30 Jun 2020 00:58:05: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:58:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:58:05: #1 tags after filtering in treatment: 12561473 INFO @ Tue, 30 Jun 2020 00:58:05: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 30 Jun 2020 00:58:05: #1 finished! INFO @ Tue, 30 Jun 2020 00:58:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:58:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:58:06: #2 number of paired peaks: 71 WARNING @ Tue, 30 Jun 2020 00:58:06: Too few paired peaks (71) 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 @ Tue, 30 Jun 2020 00:58:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474606/SRX474606.10_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/SRX474606/SRX474606.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474606/SRX474606.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474606/SRX474606.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:58:09: 26000000 INFO @ Tue, 30 Jun 2020 00:58:15: 27000000 INFO @ Tue, 30 Jun 2020 00:58:22: 28000000 INFO @ Tue, 30 Jun 2020 00:58:28: 29000000 INFO @ Tue, 30 Jun 2020 00:58:32: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:58:32: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:58:32: #1 total tags in treatment: 14452710 INFO @ Tue, 30 Jun 2020 00:58:32: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:58:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:58:32: #1 tags after filtering in treatment: 12561473 INFO @ Tue, 30 Jun 2020 00:58:32: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 30 Jun 2020 00:58:32: #1 finished! INFO @ Tue, 30 Jun 2020 00:58:32: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:58:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:58:33: #2 number of paired peaks: 71 WARNING @ Tue, 30 Jun 2020 00:58:33: Too few paired peaks (71) 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 @ Tue, 30 Jun 2020 00:58:33: Process for pairing-model is terminated! BigWig に変換しました。 cut: /home/okishinya/chipatlas/results/dm3/SRX474606/SRX474606.20_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/SRX474606/SRX474606.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474606/SRX474606.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474606/SRX474606.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling