Job ID = 6527652 SRX = SRX1847050 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:44:00 prefetch.2.10.7: 1) Downloading 'SRR3669867'... 2020-06-29T13:44:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:02:59 prefetch.2.10.7: HTTPS download failed 2020-06-29T14:02:59 prefetch.2.10.7: 1) failed to download SRR3669867 2020-06-29T14:03:13 prefetch.2.10.7: 1) Downloading 'SRR3669867'... 2020-06-29T14:03:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:03:13 prefetch.2.10.7: Continue download of 'SRR3669867' from 1597810973 2020-06-29T14:03:18 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:03:18 prefetch.2.10.7: 1) 'SRR3669867' was downloaded successfully Read 36399187 spots for SRR3669867/SRR3669867.sra Written 36399187 spots for SRR3669867/SRR3669867.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: 00:13:09 36399187 reads; of these: 36399187 (100.00%) were unpaired; of these: 1065034 (2.93%) aligned 0 times 24043812 (66.06%) aligned exactly 1 time 11290341 (31.02%) aligned >1 times 97.07% overall alignment rate Time searching: 00:13:09 Overall time: 00:13:09 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_rmdupse_core] 12663637 / 35334153 = 0.3584 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 23:34:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1847050/SRX1847050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1847050/SRX1847050.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1847050/SRX1847050.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1847050/SRX1847050.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 23:34:10: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:34:10: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:34:16: 1000000 INFO @ Mon, 29 Jun 2020 23:34:21: 2000000 INFO @ Mon, 29 Jun 2020 23:34:26: 3000000 INFO @ Mon, 29 Jun 2020 23:34:31: 4000000 INFO @ Mon, 29 Jun 2020 23:34:36: 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 23:34:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1847050/SRX1847050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1847050/SRX1847050.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1847050/SRX1847050.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1847050/SRX1847050.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 23:34:40: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:34:40: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:34:41: 6000000 INFO @ Mon, 29 Jun 2020 23:34:46: 7000000 INFO @ Mon, 29 Jun 2020 23:34:47: 1000000 INFO @ Mon, 29 Jun 2020 23:34:52: 8000000 INFO @ Mon, 29 Jun 2020 23:34:52: 2000000 INFO @ Mon, 29 Jun 2020 23:34:57: 9000000 INFO @ Mon, 29 Jun 2020 23:34:58: 3000000 INFO @ Mon, 29 Jun 2020 23:35:02: 10000000 INFO @ Mon, 29 Jun 2020 23:35:03: 4000000 INFO @ Mon, 29 Jun 2020 23:35:08: 11000000 INFO @ Mon, 29 Jun 2020 23:35:08: 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 23:35:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1847050/SRX1847050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1847050/SRX1847050.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1847050/SRX1847050.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1847050/SRX1847050.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 23:35:11: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:35:11: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:35:13: 12000000 INFO @ Mon, 29 Jun 2020 23:35:14: 6000000 INFO @ Mon, 29 Jun 2020 23:35:17: 1000000 INFO @ Mon, 29 Jun 2020 23:35:19: 13000000 INFO @ Mon, 29 Jun 2020 23:35:19: 7000000 INFO @ Mon, 29 Jun 2020 23:35:24: 2000000 INFO @ Mon, 29 Jun 2020 23:35:24: 14000000 INFO @ Mon, 29 Jun 2020 23:35:25: 8000000 INFO @ Mon, 29 Jun 2020 23:35:30: 15000000 INFO @ Mon, 29 Jun 2020 23:35:30: 3000000 INFO @ Mon, 29 Jun 2020 23:35:30: 9000000 INFO @ Mon, 29 Jun 2020 23:35:35: 16000000 INFO @ Mon, 29 Jun 2020 23:35:36: 10000000 INFO @ Mon, 29 Jun 2020 23:35:36: 4000000 INFO @ Mon, 29 Jun 2020 23:35:41: 17000000 INFO @ Mon, 29 Jun 2020 23:35:41: 11000000 INFO @ Mon, 29 Jun 2020 23:35:43: 5000000 INFO @ Mon, 29 Jun 2020 23:35:47: 18000000 INFO @ Mon, 29 Jun 2020 23:35:47: 12000000 INFO @ Mon, 29 Jun 2020 23:35:49: 6000000 INFO @ Mon, 29 Jun 2020 23:35:52: 19000000 INFO @ Mon, 29 Jun 2020 23:35:52: 13000000 INFO @ Mon, 29 Jun 2020 23:35:55: 7000000 INFO @ Mon, 29 Jun 2020 23:35:58: 20000000 INFO @ Mon, 29 Jun 2020 23:35:58: 14000000 INFO @ Mon, 29 Jun 2020 23:36:02: 8000000 INFO @ Mon, 29 Jun 2020 23:36:03: 21000000 INFO @ Mon, 29 Jun 2020 23:36:04: 15000000 INFO @ Mon, 29 Jun 2020 23:36:08: 9000000 INFO @ Mon, 29 Jun 2020 23:36:09: 22000000 INFO @ Mon, 29 Jun 2020 23:36:10: 16000000 INFO @ Mon, 29 Jun 2020 23:36:13: #1 tag size is determined as 49 bps INFO @ Mon, 29 Jun 2020 23:36:13: #1 tag size = 49 INFO @ Mon, 29 Jun 2020 23:36:13: #1 total tags in treatment: 22670516 INFO @ Mon, 29 Jun 2020 23:36:13: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:36:13: #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 23:36:14: #1 tags after filtering in treatment: 22670516 INFO @ Mon, 29 Jun 2020 23:36:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:36:14: #1 finished! INFO @ Mon, 29 Jun 2020 23:36:14: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:36:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:36:15: 10000000 INFO @ Mon, 29 Jun 2020 23:36:15: #2 number of paired peaks: 9 WARNING @ Mon, 29 Jun 2020 23:36:15: Too few paired peaks (9) 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 23:36:15: Process for pairing-model is terminated! INFO @ Mon, 29 Jun 2020 23:36:15: 17000000 cut: /home/okishinya/chipatlas/results/dm3/SRX1847050/SRX1847050.05_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/SRX1847050/SRX1847050.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1847050/SRX1847050.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1847050/SRX1847050.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:36:21: 18000000 INFO @ Mon, 29 Jun 2020 23:36:21: 11000000 INFO @ Mon, 29 Jun 2020 23:36:26: 19000000 INFO @ Mon, 29 Jun 2020 23:36:27: 12000000 INFO @ Mon, 29 Jun 2020 23:36:32: 20000000 INFO @ Mon, 29 Jun 2020 23:36:34: 13000000 INFO @ Mon, 29 Jun 2020 23:36:37: 21000000 INFO @ Mon, 29 Jun 2020 23:36:40: 14000000 INFO @ Mon, 29 Jun 2020 23:36:43: 22000000 INFO @ Mon, 29 Jun 2020 23:36:47: 15000000 INFO @ Mon, 29 Jun 2020 23:36:47: #1 tag size is determined as 49 bps INFO @ Mon, 29 Jun 2020 23:36:47: #1 tag size = 49 INFO @ Mon, 29 Jun 2020 23:36:47: #1 total tags in treatment: 22670516 INFO @ Mon, 29 Jun 2020 23:36:47: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:36:47: #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 23:36:47: #1 tags after filtering in treatment: 22670516 INFO @ Mon, 29 Jun 2020 23:36:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:36:47: #1 finished! INFO @ Mon, 29 Jun 2020 23:36:47: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:36:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:36:49: #2 number of paired peaks: 9 WARNING @ Mon, 29 Jun 2020 23:36:49: Too few paired peaks (9) 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 23:36:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1847050/SRX1847050.10_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/SRX1847050/SRX1847050.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1847050/SRX1847050.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1847050/SRX1847050.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:36:53: 16000000 INFO @ Mon, 29 Jun 2020 23:36:59: 17000000 INFO @ Mon, 29 Jun 2020 23:37:05: 18000000 INFO @ Mon, 29 Jun 2020 23:37:12: 19000000 INFO @ Mon, 29 Jun 2020 23:37:18: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:37:24: 21000000 INFO @ Mon, 29 Jun 2020 23:37:30: 22000000 INFO @ Mon, 29 Jun 2020 23:37:35: #1 tag size is determined as 49 bps INFO @ Mon, 29 Jun 2020 23:37:35: #1 tag size = 49 INFO @ Mon, 29 Jun 2020 23:37:35: #1 total tags in treatment: 22670516 INFO @ Mon, 29 Jun 2020 23:37:35: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:37:35: #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 23:37:35: #1 tags after filtering in treatment: 22670516 INFO @ Mon, 29 Jun 2020 23:37:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:37:35: #1 finished! INFO @ Mon, 29 Jun 2020 23:37:35: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:37:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:37:37: #2 number of paired peaks: 9 WARNING @ Mon, 29 Jun 2020 23:37:37: Too few paired peaks (9) 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 23:37:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1847050/SRX1847050.20_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/SRX1847050/SRX1847050.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1847050/SRX1847050.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1847050/SRX1847050.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。