Job ID = 14519682 SRX = SRX9067172 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4025159 spots for SRR12580325/SRR12580325.sra Written 4025159 spots for SRR12580325/SRR12580325.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: 00:01:35 4025159 reads; of these: 4025159 (100.00%) were paired; of these: 497653 (12.36%) aligned concordantly 0 times 3318799 (82.45%) aligned concordantly exactly 1 time 208707 (5.19%) aligned concordantly >1 times ---- 497653 pairs aligned concordantly 0 times; of these: 186032 (37.38%) aligned discordantly 1 time ---- 311621 pairs aligned 0 times concordantly or discordantly; of these: 623242 mates make up the pairs; of these: 424989 (68.19%) aligned 0 times 166494 (26.71%) aligned exactly 1 time 31759 (5.10%) aligned >1 times 94.72% overall alignment rate Time searching: 00:01:35 Overall time: 00:01:35 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] 529281 / 3612056 = 0.1465 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 17:25:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067172/SRX9067172.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067172/SRX9067172.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067172/SRX9067172.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067172/SRX9067172.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 @ Sat, 15 Jan 2022 17:25:30: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:25:30: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:25:34: 1000000 INFO @ Sat, 15 Jan 2022 17:25:39: 2000000 INFO @ Sat, 15 Jan 2022 17:25:43: 3000000 INFO @ Sat, 15 Jan 2022 17:25:47: 4000000 INFO @ Sat, 15 Jan 2022 17:25:52: 5000000 INFO @ Sat, 15 Jan 2022 17:25:56: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 17:25:59: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 17:25:59: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 17:25:59: #1 total tags in treatment: 3004644 INFO @ Sat, 15 Jan 2022 17:25:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:25:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 17:25:59: #1 tags after filtering in treatment: 2070511 INFO @ Sat, 15 Jan 2022 17:25:59: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Jan 2022 17:25:59: #1 finished! INFO @ Sat, 15 Jan 2022 17:25:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:25:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:25:59: #2 number of paired peaks: 0 WARNING @ Sat, 15 Jan 2022 17:25:59: Too few paired peaks (0) 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 @ Sat, 15 Jan 2022 17:25:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067172/SRX9067172.05_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/SRX9067172/SRX9067172.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067172/SRX9067172.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067172/SRX9067172.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:26:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067172/SRX9067172.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067172/SRX9067172.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067172/SRX9067172.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067172/SRX9067172.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 @ Sat, 15 Jan 2022 17:26:00: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:26:00: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:26:06: 1000000 INFO @ Sat, 15 Jan 2022 17:26:12: 2000000 INFO @ Sat, 15 Jan 2022 17:26:18: 3000000 INFO @ Sat, 15 Jan 2022 17:26:23: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 17:26:29: 5000000 INFO @ Sat, 15 Jan 2022 17:26:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067172/SRX9067172.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067172/SRX9067172.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067172/SRX9067172.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067172/SRX9067172.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 @ Sat, 15 Jan 2022 17:26:30: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:26:30: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:26:35: 1000000 INFO @ Sat, 15 Jan 2022 17:26:35: 6000000 INFO @ Sat, 15 Jan 2022 17:26:39: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 17:26:39: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 17:26:39: #1 total tags in treatment: 3004644 INFO @ Sat, 15 Jan 2022 17:26:39: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:26:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 17:26:39: #1 tags after filtering in treatment: 2070511 INFO @ Sat, 15 Jan 2022 17:26:39: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Jan 2022 17:26:39: #1 finished! INFO @ Sat, 15 Jan 2022 17:26:39: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:26:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:26:39: #2 number of paired peaks: 0 WARNING @ Sat, 15 Jan 2022 17:26:39: Too few paired peaks (0) 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 @ Sat, 15 Jan 2022 17:26:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067172/SRX9067172.10_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/sacCer3/SRX9067172/SRX9067172.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067172/SRX9067172.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067172/SRX9067172.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:26:40: 2000000 INFO @ Sat, 15 Jan 2022 17:26:45: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:26:50: 4000000 INFO @ Sat, 15 Jan 2022 17:26:56: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:27:01: 6000000 INFO @ Sat, 15 Jan 2022 17:27:04: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 17:27:04: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 17:27:04: #1 total tags in treatment: 3004644 INFO @ Sat, 15 Jan 2022 17:27:04: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:27:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 17:27:04: #1 tags after filtering in treatment: 2070511 INFO @ Sat, 15 Jan 2022 17:27:04: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Jan 2022 17:27:04: #1 finished! INFO @ Sat, 15 Jan 2022 17:27:04: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:27:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:27:04: #2 number of paired peaks: 0 WARNING @ Sat, 15 Jan 2022 17:27:04: Too few paired peaks (0) 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 @ Sat, 15 Jan 2022 17:27:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067172/SRX9067172.20_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/SRX9067172/SRX9067172.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067172/SRX9067172.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067172/SRX9067172.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling