Job ID = 6527655 SRX = SRX1929542 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T13:37:58 prefetch.2.10.7: 1) Downloading 'SRR3845161'... 2020-06-29T13:37:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:46:20 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:46:20 prefetch.2.10.7: 1) 'SRR3845161' was downloaded successfully Read 9173277 spots for SRR3845161/SRR3845161.sra Written 9173277 spots for SRR3845161/SRR3845161.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: 00:22:31 9173277 reads; of these: 9173277 (100.00%) were paired; of these: 743106 (8.10%) aligned concordantly 0 times 7201456 (78.50%) aligned concordantly exactly 1 time 1228715 (13.39%) aligned concordantly >1 times ---- 743106 pairs aligned concordantly 0 times; of these: 92372 (12.43%) aligned discordantly 1 time ---- 650734 pairs aligned 0 times concordantly or discordantly; of these: 1301468 mates make up the pairs; of these: 1053459 (80.94%) aligned 0 times 179337 (13.78%) aligned exactly 1 time 68672 (5.28%) aligned >1 times 94.26% overall alignment rate Time searching: 00:22:31 Overall time: 00:22:31 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] 100409 / 8492643 = 0.0118 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 23:32:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1929542/SRX1929542.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1929542/SRX1929542.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1929542/SRX1929542.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1929542/SRX1929542.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 23:32:09: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:32:09: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:32:15: 1000000 INFO @ Mon, 29 Jun 2020 23:32:21: 2000000 INFO @ Mon, 29 Jun 2020 23:32:27: 3000000 INFO @ Mon, 29 Jun 2020 23:32:33: 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 23:32:39: 5000000 INFO @ Mon, 29 Jun 2020 23:32:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1929542/SRX1929542.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1929542/SRX1929542.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1929542/SRX1929542.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1929542/SRX1929542.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 23:32:39: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:32:39: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:32:45: 6000000 INFO @ Mon, 29 Jun 2020 23:32:46: 1000000 INFO @ Mon, 29 Jun 2020 23:32:51: 7000000 INFO @ Mon, 29 Jun 2020 23:32:52: 2000000 INFO @ Mon, 29 Jun 2020 23:32:57: 8000000 INFO @ Mon, 29 Jun 2020 23:32:58: 3000000 INFO @ Mon, 29 Jun 2020 23:33:03: 9000000 INFO @ Mon, 29 Jun 2020 23:33:04: 4000000 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 23:33:09: 10000000 INFO @ Mon, 29 Jun 2020 23:33:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1929542/SRX1929542.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1929542/SRX1929542.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1929542/SRX1929542.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1929542/SRX1929542.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 23:33:09: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:33:09: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:33:11: 5000000 INFO @ Mon, 29 Jun 2020 23:33:15: 11000000 INFO @ Mon, 29 Jun 2020 23:33:17: 1000000 INFO @ Mon, 29 Jun 2020 23:33:18: 6000000 INFO @ Mon, 29 Jun 2020 23:33:21: 12000000 INFO @ Mon, 29 Jun 2020 23:33:24: 2000000 INFO @ Mon, 29 Jun 2020 23:33:25: 7000000 INFO @ Mon, 29 Jun 2020 23:33:27: 13000000 INFO @ Mon, 29 Jun 2020 23:33:31: 3000000 INFO @ Mon, 29 Jun 2020 23:33:32: 8000000 INFO @ Mon, 29 Jun 2020 23:33:34: 14000000 INFO @ Mon, 29 Jun 2020 23:33:38: 4000000 INFO @ Mon, 29 Jun 2020 23:33:39: 9000000 INFO @ Mon, 29 Jun 2020 23:33:40: 15000000 INFO @ Mon, 29 Jun 2020 23:33:45: 5000000 INFO @ Mon, 29 Jun 2020 23:33:46: 16000000 INFO @ Mon, 29 Jun 2020 23:33:46: 10000000 INFO @ Mon, 29 Jun 2020 23:33:52: 17000000 INFO @ Mon, 29 Jun 2020 23:33:52: 6000000 INFO @ Mon, 29 Jun 2020 23:33:53: #1 tag size is determined as 101 bps INFO @ Mon, 29 Jun 2020 23:33:53: #1 tag size = 101 INFO @ Mon, 29 Jun 2020 23:33:53: #1 total tags in treatment: 8329836 INFO @ Mon, 29 Jun 2020 23:33:53: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:33:53: #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 23:33:53: #1 tags after filtering in treatment: 7913459 INFO @ Mon, 29 Jun 2020 23:33:53: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 29 Jun 2020 23:33:53: #1 finished! INFO @ Mon, 29 Jun 2020 23:33:53: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:33:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:33:53: 11000000 INFO @ Mon, 29 Jun 2020 23:33:53: #2 number of paired peaks: 61 WARNING @ Mon, 29 Jun 2020 23:33:53: Too few paired peaks (61) 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 23:33:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1929542/SRX1929542.05_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/SRX1929542/SRX1929542.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1929542/SRX1929542.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1929542/SRX1929542.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:33:59: 7000000 INFO @ Mon, 29 Jun 2020 23:34:00: 12000000 INFO @ Mon, 29 Jun 2020 23:34:06: 8000000 INFO @ Mon, 29 Jun 2020 23:34:07: 13000000 INFO @ Mon, 29 Jun 2020 23:34:13: 9000000 INFO @ Mon, 29 Jun 2020 23:34:14: 14000000 INFO @ Mon, 29 Jun 2020 23:34:20: 10000000 INFO @ Mon, 29 Jun 2020 23:34:21: 15000000 INFO @ Mon, 29 Jun 2020 23:34:27: 11000000 INFO @ Mon, 29 Jun 2020 23:34:28: 16000000 INFO @ Mon, 29 Jun 2020 23:34:34: 12000000 INFO @ Mon, 29 Jun 2020 23:34:35: 17000000 INFO @ Mon, 29 Jun 2020 23:34:36: #1 tag size is determined as 101 bps INFO @ Mon, 29 Jun 2020 23:34:36: #1 tag size = 101 INFO @ Mon, 29 Jun 2020 23:34:36: #1 total tags in treatment: 8329836 INFO @ Mon, 29 Jun 2020 23:34:36: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:34:36: #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 23:34:36: #1 tags after filtering in treatment: 7913459 INFO @ Mon, 29 Jun 2020 23:34:36: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 29 Jun 2020 23:34:36: #1 finished! INFO @ Mon, 29 Jun 2020 23:34:36: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:34:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:34:37: #2 number of paired peaks: 61 WARNING @ Mon, 29 Jun 2020 23:34:37: Too few paired peaks (61) 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 23:34:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1929542/SRX1929542.10_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/SRX1929542/SRX1929542.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1929542/SRX1929542.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1929542/SRX1929542.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:34:41: 13000000 INFO @ Mon, 29 Jun 2020 23:34:47: 14000000 INFO @ Mon, 29 Jun 2020 23:34:53: 15000000 INFO @ Mon, 29 Jun 2020 23:34:59: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:35:05: 17000000 INFO @ Mon, 29 Jun 2020 23:35:06: #1 tag size is determined as 101 bps INFO @ Mon, 29 Jun 2020 23:35:06: #1 tag size = 101 INFO @ Mon, 29 Jun 2020 23:35:06: #1 total tags in treatment: 8329836 INFO @ Mon, 29 Jun 2020 23:35:06: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:35:06: #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 23:35:06: #1 tags after filtering in treatment: 7913459 INFO @ Mon, 29 Jun 2020 23:35:06: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 29 Jun 2020 23:35:06: #1 finished! INFO @ Mon, 29 Jun 2020 23:35:06: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:35:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:35:07: #2 number of paired peaks: 61 WARNING @ Mon, 29 Jun 2020 23:35:07: Too few paired peaks (61) 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 23:35:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1929542/SRX1929542.20_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/SRX1929542/SRX1929542.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1929542/SRX1929542.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1929542/SRX1929542.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。