Job ID = 10223919 SRX = SRX4623309 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8011686 spots for SRR7767714/SRR7767714.sra Written 8011686 spots for SRR7767714/SRR7767714.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: 00:02:33 8011686 reads; of these: 8011686 (100.00%) were paired; of these: 627628 (7.83%) aligned concordantly 0 times 1396186 (17.43%) aligned concordantly exactly 1 time 5987872 (74.74%) aligned concordantly >1 times ---- 627628 pairs aligned concordantly 0 times; of these: 24673 (3.93%) aligned discordantly 1 time ---- 602955 pairs aligned 0 times concordantly or discordantly; of these: 1205910 mates make up the pairs; of these: 944083 (78.29%) aligned 0 times 27159 (2.25%) aligned exactly 1 time 234668 (19.46%) aligned >1 times 94.11% overall alignment rate Time searching: 00:02:33 Overall time: 00:02:33 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_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] 3107796 / 7408109 = 0.4195 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 08:50:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4623309/SRX4623309.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4623309/SRX4623309.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4623309/SRX4623309.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4623309/SRX4623309.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 08:50:49: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:50:49: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:50:53: 1000000 INFO @ Fri, 16 Oct 2020 08:50:57: 2000000 INFO @ Fri, 16 Oct 2020 08:51:00: 3000000 INFO @ Fri, 16 Oct 2020 08:51:04: 4000000 INFO @ Fri, 16 Oct 2020 08:51:08: 5000000 INFO @ Fri, 16 Oct 2020 08:51:11: 6000000 INFO @ Fri, 16 Oct 2020 08:51:15: 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 08:51:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4623309/SRX4623309.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4623309/SRX4623309.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4623309/SRX4623309.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4623309/SRX4623309.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 08:51:19: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:51:19: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:51:19: 8000000 INFO @ Fri, 16 Oct 2020 08:51:22: #1 tag size is determined as 25 bps INFO @ Fri, 16 Oct 2020 08:51:22: #1 tag size = 25 INFO @ Fri, 16 Oct 2020 08:51:22: #1 total tags in treatment: 4276663 INFO @ Fri, 16 Oct 2020 08:51:22: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:51:22: #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 08:51:22: #1 tags after filtering in treatment: 1442412 INFO @ Fri, 16 Oct 2020 08:51:22: #1 Redundant rate of treatment: 0.66 INFO @ Fri, 16 Oct 2020 08:51:22: #1 finished! INFO @ Fri, 16 Oct 2020 08:51:22: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:51:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:51:22: #2 number of paired peaks: 33 WARNING @ Fri, 16 Oct 2020 08:51:22: Too few paired peaks (33) 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 08:51:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4623309/SRX4623309.05_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/SRX4623309/SRX4623309.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4623309/SRX4623309.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4623309/SRX4623309.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:51:23: 1000000 INFO @ Fri, 16 Oct 2020 08:51:28: 2000000 INFO @ Fri, 16 Oct 2020 08:51:32: 3000000 INFO @ Fri, 16 Oct 2020 08:51:36: 4000000 INFO @ Fri, 16 Oct 2020 08:51:41: 5000000 INFO @ Fri, 16 Oct 2020 08:51:45: 6000000 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 08:51:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4623309/SRX4623309.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4623309/SRX4623309.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4623309/SRX4623309.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4623309/SRX4623309.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 08:51:49: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:51:49: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:51:49: 7000000 INFO @ Fri, 16 Oct 2020 08:51:53: 1000000 INFO @ Fri, 16 Oct 2020 08:51:53: 8000000 INFO @ Fri, 16 Oct 2020 08:51:57: #1 tag size is determined as 25 bps INFO @ Fri, 16 Oct 2020 08:51:57: #1 tag size = 25 INFO @ Fri, 16 Oct 2020 08:51:57: #1 total tags in treatment: 4276663 INFO @ Fri, 16 Oct 2020 08:51:57: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:51:57: #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 08:51:57: #1 tags after filtering in treatment: 1442412 INFO @ Fri, 16 Oct 2020 08:51:57: #1 Redundant rate of treatment: 0.66 INFO @ Fri, 16 Oct 2020 08:51:57: #1 finished! INFO @ Fri, 16 Oct 2020 08:51:57: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:51:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:51:57: #2 number of paired peaks: 33 WARNING @ Fri, 16 Oct 2020 08:51:57: Too few paired peaks (33) 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 08:51:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4623309/SRX4623309.10_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/SRX4623309/SRX4623309.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4623309/SRX4623309.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4623309/SRX4623309.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:51:57: 2000000 INFO @ Fri, 16 Oct 2020 08:52:02: 3000000 INFO @ Fri, 16 Oct 2020 08:52:06: 4000000 INFO @ Fri, 16 Oct 2020 08:52:10: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:52:15: 6000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:52:19: 7000000 INFO @ Fri, 16 Oct 2020 08:52:23: 8000000 INFO @ Fri, 16 Oct 2020 08:52:27: #1 tag size is determined as 25 bps INFO @ Fri, 16 Oct 2020 08:52:27: #1 tag size = 25 INFO @ Fri, 16 Oct 2020 08:52:27: #1 total tags in treatment: 4276663 INFO @ Fri, 16 Oct 2020 08:52:27: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:52:27: #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 08:52:27: #1 tags after filtering in treatment: 1442412 INFO @ Fri, 16 Oct 2020 08:52:27: #1 Redundant rate of treatment: 0.66 INFO @ Fri, 16 Oct 2020 08:52:27: #1 finished! INFO @ Fri, 16 Oct 2020 08:52:27: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:52:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:52:27: #2 number of paired peaks: 33 WARNING @ Fri, 16 Oct 2020 08:52:27: Too few paired peaks (33) 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 08:52:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4623309/SRX4623309.20_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/SRX4623309/SRX4623309.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4623309/SRX4623309.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4623309/SRX4623309.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling