Job ID = 6527644 SRX = SRX183888 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:21:23 prefetch.2.10.7: 1) Downloading 'SRR557683'... 2020-06-29T13:21:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:26:30 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:26:30 prefetch.2.10.7: 1) 'SRR557683' was downloaded successfully Read 35738149 spots for SRR557683/SRR557683.sra Written 35738149 spots for SRR557683/SRR557683.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: 00:12:44 35738149 reads; of these: 35738149 (100.00%) were unpaired; of these: 935910 (2.62%) aligned 0 times 24220447 (67.77%) aligned exactly 1 time 10581792 (29.61%) aligned >1 times 97.38% overall alignment rate Time searching: 00:12:44 Overall time: 00:12:44 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] 6474277 / 34802239 = 0.1860 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 22:57:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX183888/SRX183888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX183888/SRX183888.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX183888/SRX183888.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX183888/SRX183888.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 22:57:09: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:57:09: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:57:14: 1000000 INFO @ Mon, 29 Jun 2020 22:57:20: 2000000 INFO @ Mon, 29 Jun 2020 22:57:25: 3000000 INFO @ Mon, 29 Jun 2020 22:57:30: 4000000 INFO @ Mon, 29 Jun 2020 22:57:36: 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 22:57:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX183888/SRX183888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX183888/SRX183888.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX183888/SRX183888.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX183888/SRX183888.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 22:57:39: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:57:39: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:57:41: 6000000 INFO @ Mon, 29 Jun 2020 22:57:44: 1000000 INFO @ Mon, 29 Jun 2020 22:57:46: 7000000 INFO @ Mon, 29 Jun 2020 22:57:48: 2000000 INFO @ Mon, 29 Jun 2020 22:57:52: 8000000 INFO @ Mon, 29 Jun 2020 22:57:53: 3000000 INFO @ Mon, 29 Jun 2020 22:57:57: 9000000 INFO @ Mon, 29 Jun 2020 22:57:58: 4000000 INFO @ Mon, 29 Jun 2020 22:58:03: 10000000 INFO @ Mon, 29 Jun 2020 22:58:03: 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 22:58:07: 6000000 INFO @ Mon, 29 Jun 2020 22:58:08: 11000000 INFO @ Mon, 29 Jun 2020 22:58:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX183888/SRX183888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX183888/SRX183888.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX183888/SRX183888.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX183888/SRX183888.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 22:58:09: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:58:09: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:58:12: 7000000 INFO @ Mon, 29 Jun 2020 22:58:13: 12000000 INFO @ Mon, 29 Jun 2020 22:58:14: 1000000 INFO @ Mon, 29 Jun 2020 22:58:17: 8000000 INFO @ Mon, 29 Jun 2020 22:58:19: 13000000 INFO @ Mon, 29 Jun 2020 22:58:20: 2000000 INFO @ Mon, 29 Jun 2020 22:58:21: 9000000 INFO @ Mon, 29 Jun 2020 22:58:24: 14000000 INFO @ Mon, 29 Jun 2020 22:58:25: 3000000 INFO @ Mon, 29 Jun 2020 22:58:26: 10000000 INFO @ Mon, 29 Jun 2020 22:58:30: 15000000 INFO @ Mon, 29 Jun 2020 22:58:31: 11000000 INFO @ Mon, 29 Jun 2020 22:58:31: 4000000 INFO @ Mon, 29 Jun 2020 22:58:35: 16000000 INFO @ Mon, 29 Jun 2020 22:58:36: 12000000 INFO @ Mon, 29 Jun 2020 22:58:36: 5000000 INFO @ Mon, 29 Jun 2020 22:58:40: 13000000 INFO @ Mon, 29 Jun 2020 22:58:41: 17000000 INFO @ Mon, 29 Jun 2020 22:58:42: 6000000 INFO @ Mon, 29 Jun 2020 22:58:45: 14000000 INFO @ Mon, 29 Jun 2020 22:58:47: 18000000 INFO @ Mon, 29 Jun 2020 22:58:48: 7000000 INFO @ Mon, 29 Jun 2020 22:58:50: 15000000 INFO @ Mon, 29 Jun 2020 22:58:52: 19000000 INFO @ Mon, 29 Jun 2020 22:58:53: 8000000 INFO @ Mon, 29 Jun 2020 22:58:55: 16000000 INFO @ Mon, 29 Jun 2020 22:58:57: 20000000 INFO @ Mon, 29 Jun 2020 22:58:59: 9000000 INFO @ Mon, 29 Jun 2020 22:58:59: 17000000 INFO @ Mon, 29 Jun 2020 22:59:03: 21000000 INFO @ Mon, 29 Jun 2020 22:59:04: 18000000 INFO @ Mon, 29 Jun 2020 22:59:04: 10000000 INFO @ Mon, 29 Jun 2020 22:59:08: 22000000 INFO @ Mon, 29 Jun 2020 22:59:09: 19000000 INFO @ Mon, 29 Jun 2020 22:59:10: 11000000 INFO @ Mon, 29 Jun 2020 22:59:14: 20000000 INFO @ Mon, 29 Jun 2020 22:59:14: 23000000 INFO @ Mon, 29 Jun 2020 22:59:15: 12000000 INFO @ Mon, 29 Jun 2020 22:59:19: 21000000 INFO @ Mon, 29 Jun 2020 22:59:19: 24000000 INFO @ Mon, 29 Jun 2020 22:59:21: 13000000 INFO @ Mon, 29 Jun 2020 22:59:23: 22000000 INFO @ Mon, 29 Jun 2020 22:59:25: 25000000 INFO @ Mon, 29 Jun 2020 22:59:27: 14000000 INFO @ Mon, 29 Jun 2020 22:59:28: 23000000 INFO @ Mon, 29 Jun 2020 22:59:30: 26000000 INFO @ Mon, 29 Jun 2020 22:59:32: 15000000 INFO @ Mon, 29 Jun 2020 22:59:33: 24000000 INFO @ Mon, 29 Jun 2020 22:59:36: 27000000 INFO @ Mon, 29 Jun 2020 22:59:37: 25000000 INFO @ Mon, 29 Jun 2020 22:59:38: 16000000 INFO @ Mon, 29 Jun 2020 22:59:41: 28000000 INFO @ Mon, 29 Jun 2020 22:59:42: 26000000 INFO @ Mon, 29 Jun 2020 22:59:43: #1 tag size is determined as 40 bps INFO @ Mon, 29 Jun 2020 22:59:43: #1 tag size = 40 INFO @ Mon, 29 Jun 2020 22:59:43: #1 total tags in treatment: 28327962 INFO @ Mon, 29 Jun 2020 22:59:43: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:59:43: #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 22:59:43: 17000000 INFO @ Mon, 29 Jun 2020 22:59:44: #1 tags after filtering in treatment: 28327962 INFO @ Mon, 29 Jun 2020 22:59:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:59:44: #1 finished! INFO @ Mon, 29 Jun 2020 22:59:44: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:59:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:59:46: #2 number of paired peaks: 37 WARNING @ Mon, 29 Jun 2020 22:59:46: Too few paired peaks (37) 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 22:59:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX183888/SRX183888.05_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/SRX183888/SRX183888.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX183888/SRX183888.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX183888/SRX183888.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:59:47: 27000000 INFO @ Mon, 29 Jun 2020 22:59:49: 18000000 INFO @ Mon, 29 Jun 2020 22:59:52: 28000000 INFO @ Mon, 29 Jun 2020 22:59:54: #1 tag size is determined as 40 bps INFO @ Mon, 29 Jun 2020 22:59:54: #1 tag size = 40 INFO @ Mon, 29 Jun 2020 22:59:54: #1 total tags in treatment: 28327962 INFO @ Mon, 29 Jun 2020 22:59:54: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:59:54: #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 22:59:54: #1 tags after filtering in treatment: 28327962 INFO @ Mon, 29 Jun 2020 22:59:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:59:54: #1 finished! INFO @ Mon, 29 Jun 2020 22:59:54: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:59:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:59:54: 19000000 INFO @ Mon, 29 Jun 2020 22:59:56: #2 number of paired peaks: 37 WARNING @ Mon, 29 Jun 2020 22:59:56: Too few paired peaks (37) 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 22:59:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX183888/SRX183888.10_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/SRX183888/SRX183888.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX183888/SRX183888.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX183888/SRX183888.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:00:00: 20000000 INFO @ Mon, 29 Jun 2020 23:00:05: 21000000 INFO @ Mon, 29 Jun 2020 23:00:10: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:00:16: 23000000 INFO @ Mon, 29 Jun 2020 23:00:21: 24000000 INFO @ Mon, 29 Jun 2020 23:00:26: 25000000 INFO @ Mon, 29 Jun 2020 23:00:32: 26000000 INFO @ Mon, 29 Jun 2020 23:00:37: 27000000 INFO @ Mon, 29 Jun 2020 23:00:42: 28000000 INFO @ Mon, 29 Jun 2020 23:00:44: #1 tag size is determined as 40 bps INFO @ Mon, 29 Jun 2020 23:00:44: #1 tag size = 40 INFO @ Mon, 29 Jun 2020 23:00:44: #1 total tags in treatment: 28327962 INFO @ Mon, 29 Jun 2020 23:00:44: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:00:44: #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 23:00:44: #1 tags after filtering in treatment: 28327962 INFO @ Mon, 29 Jun 2020 23:00:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:00:44: #1 finished! INFO @ Mon, 29 Jun 2020 23:00:44: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:00:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:00:46: #2 number of paired peaks: 37 WARNING @ Mon, 29 Jun 2020 23:00:46: Too few paired peaks (37) 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 23:00:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX183888/SRX183888.20_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/SRX183888/SRX183888.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX183888/SRX183888.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX183888/SRX183888.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。