Job ID = 6527760 SRX = SRX2659838 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:45:44 prefetch.2.10.7: 1) Downloading 'SRR5364411'... 2020-06-29T13:45:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:50:50 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:50:50 prefetch.2.10.7: 1) 'SRR5364411' was downloaded successfully 2020-06-29T13:50:50 prefetch.2.10.7: 'SRR5364411' has 0 unresolved dependencies Read 39606963 spots for SRR5364411/SRR5364411.sra Written 39606963 spots for SRR5364411/SRR5364411.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:26:18 39606963 reads; of these: 39606963 (100.00%) were unpaired; of these: 12791703 (32.30%) aligned 0 times 20627434 (52.08%) aligned exactly 1 time 6187826 (15.62%) aligned >1 times 67.70% overall alignment rate Time searching: 00:26:19 Overall time: 00:26:19 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 12 files... [bam_rmdupse_core] 4517799 / 26815260 = 0.1685 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 23:49:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2659838/SRX2659838.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2659838/SRX2659838.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2659838/SRX2659838.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2659838/SRX2659838.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 23:49:59: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:49:59: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:50:06: 1000000 INFO @ Mon, 29 Jun 2020 23:50:12: 2000000 INFO @ Mon, 29 Jun 2020 23:50:18: 3000000 INFO @ Mon, 29 Jun 2020 23:50:24: 4000000 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 23:50:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2659838/SRX2659838.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2659838/SRX2659838.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2659838/SRX2659838.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2659838/SRX2659838.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 23:50:29: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:50:29: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:50:31: 5000000 INFO @ Mon, 29 Jun 2020 23:50:37: 1000000 INFO @ Mon, 29 Jun 2020 23:50:38: 6000000 INFO @ Mon, 29 Jun 2020 23:50:44: 2000000 INFO @ Mon, 29 Jun 2020 23:50:45: 7000000 INFO @ Mon, 29 Jun 2020 23:50:51: 3000000 INFO @ Mon, 29 Jun 2020 23:50:53: 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 @ Mon, 29 Jun 2020 23:50:58: 4000000 INFO @ Mon, 29 Jun 2020 23:50:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2659838/SRX2659838.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2659838/SRX2659838.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2659838/SRX2659838.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2659838/SRX2659838.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 23:50:59: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:50:59: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:51:00: 9000000 INFO @ Mon, 29 Jun 2020 23:51:06: 5000000 INFO @ Mon, 29 Jun 2020 23:51:07: 1000000 INFO @ Mon, 29 Jun 2020 23:51:08: 10000000 INFO @ Mon, 29 Jun 2020 23:51:14: 6000000 INFO @ Mon, 29 Jun 2020 23:51:15: 2000000 INFO @ Mon, 29 Jun 2020 23:51:15: 11000000 INFO @ Mon, 29 Jun 2020 23:51:22: 7000000 INFO @ Mon, 29 Jun 2020 23:51:23: 12000000 INFO @ Mon, 29 Jun 2020 23:51:23: 3000000 INFO @ Mon, 29 Jun 2020 23:51:30: 8000000 INFO @ Mon, 29 Jun 2020 23:51:31: 13000000 INFO @ Mon, 29 Jun 2020 23:51:31: 4000000 INFO @ Mon, 29 Jun 2020 23:51:37: 9000000 INFO @ Mon, 29 Jun 2020 23:51:39: 14000000 INFO @ Mon, 29 Jun 2020 23:51:39: 5000000 INFO @ Mon, 29 Jun 2020 23:51:45: 10000000 INFO @ Mon, 29 Jun 2020 23:51:46: 15000000 INFO @ Mon, 29 Jun 2020 23:51:47: 6000000 INFO @ Mon, 29 Jun 2020 23:51:53: 11000000 INFO @ Mon, 29 Jun 2020 23:51:54: 16000000 INFO @ Mon, 29 Jun 2020 23:51:55: 7000000 INFO @ Mon, 29 Jun 2020 23:52:01: 12000000 INFO @ Mon, 29 Jun 2020 23:52:02: 17000000 INFO @ Mon, 29 Jun 2020 23:52:03: 8000000 INFO @ Mon, 29 Jun 2020 23:52:09: 13000000 INFO @ Mon, 29 Jun 2020 23:52:10: 18000000 INFO @ Mon, 29 Jun 2020 23:52:10: 9000000 INFO @ Mon, 29 Jun 2020 23:52:16: 14000000 INFO @ Mon, 29 Jun 2020 23:52:18: 19000000 INFO @ Mon, 29 Jun 2020 23:52:18: 10000000 INFO @ Mon, 29 Jun 2020 23:52:24: 15000000 INFO @ Mon, 29 Jun 2020 23:52:25: 20000000 INFO @ Mon, 29 Jun 2020 23:52:26: 11000000 INFO @ Mon, 29 Jun 2020 23:52:32: 16000000 INFO @ Mon, 29 Jun 2020 23:52:33: 21000000 INFO @ Mon, 29 Jun 2020 23:52:34: 12000000 INFO @ Mon, 29 Jun 2020 23:52:40: 17000000 INFO @ Mon, 29 Jun 2020 23:52:41: 22000000 INFO @ Mon, 29 Jun 2020 23:52:42: 13000000 INFO @ Mon, 29 Jun 2020 23:52:44: #1 tag size is determined as 76 bps INFO @ Mon, 29 Jun 2020 23:52:44: #1 tag size = 76 INFO @ Mon, 29 Jun 2020 23:52:44: #1 total tags in treatment: 22297461 INFO @ Mon, 29 Jun 2020 23:52:44: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:52:44: #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 23:52:44: #1 tags after filtering in treatment: 22297461 INFO @ Mon, 29 Jun 2020 23:52:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:52:44: #1 finished! INFO @ Mon, 29 Jun 2020 23:52:44: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:52:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:52:46: #2 number of paired peaks: 50 WARNING @ Mon, 29 Jun 2020 23:52:46: Too few paired peaks (50) 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 23:52:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX2659838/SRX2659838.05_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/SRX2659838/SRX2659838.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2659838/SRX2659838.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2659838/SRX2659838.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:52:48: 18000000 INFO @ Mon, 29 Jun 2020 23:52:49: 14000000 INFO @ Mon, 29 Jun 2020 23:52:55: 19000000 INFO @ Mon, 29 Jun 2020 23:52:56: 15000000 INFO @ Mon, 29 Jun 2020 23:53:02: 20000000 INFO @ Mon, 29 Jun 2020 23:53:04: 16000000 INFO @ Mon, 29 Jun 2020 23:53:09: 21000000 INFO @ Mon, 29 Jun 2020 23:53:11: 17000000 INFO @ Mon, 29 Jun 2020 23:53:17: 22000000 INFO @ Mon, 29 Jun 2020 23:53:18: 18000000 INFO @ Mon, 29 Jun 2020 23:53:19: #1 tag size is determined as 76 bps INFO @ Mon, 29 Jun 2020 23:53:19: #1 tag size = 76 INFO @ Mon, 29 Jun 2020 23:53:19: #1 total tags in treatment: 22297461 INFO @ Mon, 29 Jun 2020 23:53:19: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:53:19: #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 23:53:20: #1 tags after filtering in treatment: 22297461 INFO @ Mon, 29 Jun 2020 23:53:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:53:20: #1 finished! INFO @ Mon, 29 Jun 2020 23:53:20: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:53:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:53:21: #2 number of paired peaks: 50 WARNING @ Mon, 29 Jun 2020 23:53:21: Too few paired peaks (50) 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 23:53:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX2659838/SRX2659838.10_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/SRX2659838/SRX2659838.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2659838/SRX2659838.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2659838/SRX2659838.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:53:25: 19000000 INFO @ Mon, 29 Jun 2020 23:53:32: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:53:38: 21000000 INFO @ Mon, 29 Jun 2020 23:53:45: 22000000 INFO @ Mon, 29 Jun 2020 23:53:47: #1 tag size is determined as 76 bps INFO @ Mon, 29 Jun 2020 23:53:47: #1 tag size = 76 INFO @ Mon, 29 Jun 2020 23:53:47: #1 total tags in treatment: 22297461 INFO @ Mon, 29 Jun 2020 23:53:47: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:53:47: #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 23:53:47: #1 tags after filtering in treatment: 22297461 INFO @ Mon, 29 Jun 2020 23:53:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:53:47: #1 finished! INFO @ Mon, 29 Jun 2020 23:53:47: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:53:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:53:49: #2 number of paired peaks: 50 WARNING @ Mon, 29 Jun 2020 23:53:49: Too few paired peaks (50) 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 23:53:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX2659838/SRX2659838.20_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/SRX2659838/SRX2659838.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2659838/SRX2659838.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2659838/SRX2659838.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。