Job ID = 10223918 SRX = SRX4623308 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9879802 spots for SRR7767713/SRR7767713.sra Written 9879802 spots for SRR7767713/SRR7767713.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: 00:03:07 9879802 reads; of these: 9879802 (100.00%) were paired; of these: 2743943 (27.77%) aligned concordantly 0 times 4904039 (49.64%) aligned concordantly exactly 1 time 2231820 (22.59%) aligned concordantly >1 times ---- 2743943 pairs aligned concordantly 0 times; of these: 612179 (22.31%) aligned discordantly 1 time ---- 2131764 pairs aligned 0 times concordantly or discordantly; of these: 4263528 mates make up the pairs; of these: 3629491 (85.13%) aligned 0 times 187914 (4.41%) aligned exactly 1 time 446123 (10.46%) aligned >1 times 81.63% overall alignment rate Time searching: 00:03:07 Overall time: 00:03:07 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 407866 / 7744397 = 0.0527 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 @ Fri, 16 Oct 2020 08:51:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4623308/SRX4623308.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4623308/SRX4623308.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4623308/SRX4623308.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4623308/SRX4623308.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Fri, 16 Oct 2020 08:51:09: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:51:09: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:51:13: 1000000 INFO @ Fri, 16 Oct 2020 08:51:17: 2000000 INFO @ Fri, 16 Oct 2020 08:51:21: 3000000 INFO @ Fri, 16 Oct 2020 08:51:25: 4000000 INFO @ Fri, 16 Oct 2020 08:51:29: 5000000 INFO @ Fri, 16 Oct 2020 08:51:33: 6000000 INFO @ Fri, 16 Oct 2020 08:51:37: 7000000 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 @ Fri, 16 Oct 2020 08:51:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4623308/SRX4623308.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4623308/SRX4623308.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4623308/SRX4623308.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4623308/SRX4623308.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Fri, 16 Oct 2020 08:51:39: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:51:39: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:51:41: 8000000 INFO @ Fri, 16 Oct 2020 08:51:44: 1000000 INFO @ Fri, 16 Oct 2020 08:51:45: 9000000 INFO @ Fri, 16 Oct 2020 08:51:48: 2000000 INFO @ Fri, 16 Oct 2020 08:51:49: 10000000 INFO @ Fri, 16 Oct 2020 08:51:53: 3000000 INFO @ Fri, 16 Oct 2020 08:51:53: 11000000 INFO @ Fri, 16 Oct 2020 08:51:58: 12000000 INFO @ Fri, 16 Oct 2020 08:51:58: 4000000 INFO @ Fri, 16 Oct 2020 08:52:02: 13000000 INFO @ Fri, 16 Oct 2020 08:52:03: 5000000 INFO @ Fri, 16 Oct 2020 08:52:07: 14000000 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 @ Fri, 16 Oct 2020 08:52:08: 6000000 INFO @ Fri, 16 Oct 2020 08:52:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4623308/SRX4623308.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4623308/SRX4623308.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4623308/SRX4623308.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4623308/SRX4623308.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Fri, 16 Oct 2020 08:52:09: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:52:09: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:52:12: 15000000 INFO @ Fri, 16 Oct 2020 08:52:13: 7000000 INFO @ Fri, 16 Oct 2020 08:52:13: #1 tag size is determined as 25 bps INFO @ Fri, 16 Oct 2020 08:52:13: #1 tag size = 25 INFO @ Fri, 16 Oct 2020 08:52:13: #1 total tags in treatment: 6731383 INFO @ Fri, 16 Oct 2020 08:52:13: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:52:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:52:13: #1 tags after filtering in treatment: 4622453 INFO @ Fri, 16 Oct 2020 08:52:13: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 16 Oct 2020 08:52:13: #1 finished! INFO @ Fri, 16 Oct 2020 08:52:13: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:52:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:52:13: #2 number of paired peaks: 28 WARNING @ Fri, 16 Oct 2020 08:52:13: Too few paired peaks (28) 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 @ Fri, 16 Oct 2020 08:52:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4623308/SRX4623308.05_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/sacCer3/SRX4623308/SRX4623308.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4623308/SRX4623308.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4623308/SRX4623308.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:52:14: 1000000 INFO @ Fri, 16 Oct 2020 08:52:18: 8000000 INFO @ Fri, 16 Oct 2020 08:52:19: 2000000 INFO @ Fri, 16 Oct 2020 08:52:23: 9000000 INFO @ Fri, 16 Oct 2020 08:52:23: 3000000 INFO @ Fri, 16 Oct 2020 08:52:27: 4000000 INFO @ Fri, 16 Oct 2020 08:52:28: 10000000 INFO @ Fri, 16 Oct 2020 08:52:32: 5000000 INFO @ Fri, 16 Oct 2020 08:52:33: 11000000 INFO @ Fri, 16 Oct 2020 08:52:36: 6000000 INFO @ Fri, 16 Oct 2020 08:52:37: 12000000 INFO @ Fri, 16 Oct 2020 08:52:40: 7000000 INFO @ Fri, 16 Oct 2020 08:52:42: 13000000 INFO @ Fri, 16 Oct 2020 08:52:45: 8000000 INFO @ Fri, 16 Oct 2020 08:52:47: 14000000 INFO @ Fri, 16 Oct 2020 08:52:49: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:52:51: 15000000 INFO @ Fri, 16 Oct 2020 08:52:53: #1 tag size is determined as 25 bps INFO @ Fri, 16 Oct 2020 08:52:53: #1 tag size = 25 INFO @ Fri, 16 Oct 2020 08:52:53: #1 total tags in treatment: 6731383 INFO @ Fri, 16 Oct 2020 08:52:53: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:52:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:52:53: #1 tags after filtering in treatment: 4622453 INFO @ Fri, 16 Oct 2020 08:52:53: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 16 Oct 2020 08:52:53: #1 finished! INFO @ Fri, 16 Oct 2020 08:52:53: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:52:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:52:53: 10000000 INFO @ Fri, 16 Oct 2020 08:52:53: #2 number of paired peaks: 28 WARNING @ Fri, 16 Oct 2020 08:52:53: Too few paired peaks (28) 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 @ Fri, 16 Oct 2020 08:52:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4623308/SRX4623308.10_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/sacCer3/SRX4623308/SRX4623308.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4623308/SRX4623308.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4623308/SRX4623308.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:52:57: 11000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:53:01: 12000000 INFO @ Fri, 16 Oct 2020 08:53:05: 13000000 INFO @ Fri, 16 Oct 2020 08:53:10: 14000000 INFO @ Fri, 16 Oct 2020 08:53:15: 15000000 INFO @ Fri, 16 Oct 2020 08:53:16: #1 tag size is determined as 25 bps INFO @ Fri, 16 Oct 2020 08:53:16: #1 tag size = 25 INFO @ Fri, 16 Oct 2020 08:53:16: #1 total tags in treatment: 6731383 INFO @ Fri, 16 Oct 2020 08:53:16: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:53:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:53:16: #1 tags after filtering in treatment: 4622453 INFO @ Fri, 16 Oct 2020 08:53:16: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 16 Oct 2020 08:53:16: #1 finished! INFO @ Fri, 16 Oct 2020 08:53:16: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:53:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:53:16: #2 number of paired peaks: 28 WARNING @ Fri, 16 Oct 2020 08:53:16: Too few paired peaks (28) 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 @ Fri, 16 Oct 2020 08:53:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4623308/SRX4623308.20_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/sacCer3/SRX4623308/SRX4623308.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4623308/SRX4623308.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4623308/SRX4623308.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling