Job ID = 8071316 SRX = SRX7917547 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T04:26:43 prefetch.2.10.7: 1) Downloading 'SRR11313128'... 2020-08-08T04:26:43 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T04:27:13 prefetch.2.10.7: HTTPS download succeed 2020-08-08T04:27:13 prefetch.2.10.7: 'SRR11313128' is valid 2020-08-08T04:27:13 prefetch.2.10.7: 1) 'SRR11313128' was downloaded successfully Read 3718553 spots for SRR11313128/SRR11313128.sra Written 3718553 spots for SRR11313128/SRR11313128.sra fastq に変換しました。 bowtie でマッピング中... Your job 8072589 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:09 3718553 reads; of these: 3718553 (100.00%) were paired; of these: 628148 (16.89%) aligned concordantly 0 times 2353676 (63.30%) aligned concordantly exactly 1 time 736729 (19.81%) aligned concordantly >1 times ---- 628148 pairs aligned concordantly 0 times; of these: 209671 (33.38%) aligned discordantly 1 time ---- 418477 pairs aligned 0 times concordantly or discordantly; of these: 836954 mates make up the pairs; of these: 509920 (60.93%) aligned 0 times 159242 (19.03%) aligned exactly 1 time 167792 (20.05%) aligned >1 times 93.14% overall alignment rate Time searching: 00:07:09 Overall time: 00:07:09 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_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] 1107046 / 3287651 = 0.3367 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 @ Sat, 08 Aug 2020 13:36:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917547/SRX7917547.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917547/SRX7917547.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917547/SRX7917547.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917547/SRX7917547.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 @ Sat, 08 Aug 2020 13:36:32: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:36:32: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:36:38: 1000000 INFO @ Sat, 08 Aug 2020 13:36:45: 2000000 INFO @ Sat, 08 Aug 2020 13:36:52: 3000000 INFO @ Sat, 08 Aug 2020 13:36:58: 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 @ Sat, 08 Aug 2020 13:37:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917547/SRX7917547.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917547/SRX7917547.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917547/SRX7917547.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917547/SRX7917547.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 @ Sat, 08 Aug 2020 13:37:02: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:37:02: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:37:03: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:37:03: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:37:03: #1 total tags in treatment: 1999207 INFO @ Sat, 08 Aug 2020 13:37:03: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:37:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:37:03: #1 tags after filtering in treatment: 1501759 INFO @ Sat, 08 Aug 2020 13:37:03: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 08 Aug 2020 13:37:03: #1 finished! INFO @ Sat, 08 Aug 2020 13:37:03: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:37:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:37:03: #2 number of paired peaks: 4 WARNING @ Sat, 08 Aug 2020 13:37:03: Too few paired peaks (4) 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, 08 Aug 2020 13:37:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX7917547/SRX7917547.05_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/SRX7917547/SRX7917547.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917547/SRX7917547.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917547/SRX7917547.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:37:08: 1000000 INFO @ Sat, 08 Aug 2020 13:37:15: 2000000 INFO @ Sat, 08 Aug 2020 13:37:22: 3000000 INFO @ Sat, 08 Aug 2020 13:37:29: 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 @ Sat, 08 Aug 2020 13:37:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917547/SRX7917547.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917547/SRX7917547.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917547/SRX7917547.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917547/SRX7917547.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 @ Sat, 08 Aug 2020 13:37:32: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:37:32: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:37:34: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:37:34: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:37:34: #1 total tags in treatment: 1999207 INFO @ Sat, 08 Aug 2020 13:37:34: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:37:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:37:34: #1 tags after filtering in treatment: 1501759 INFO @ Sat, 08 Aug 2020 13:37:34: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 08 Aug 2020 13:37:34: #1 finished! INFO @ Sat, 08 Aug 2020 13:37:34: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:37:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:37:34: #2 number of paired peaks: 4 WARNING @ Sat, 08 Aug 2020 13:37:34: Too few paired peaks (4) 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, 08 Aug 2020 13:37:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX7917547/SRX7917547.10_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/SRX7917547/SRX7917547.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917547/SRX7917547.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917547/SRX7917547.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:37:38: 1000000 INFO @ Sat, 08 Aug 2020 13:37:45: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:37:52: 3000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:37:59: 4000000 INFO @ Sat, 08 Aug 2020 13:38:03: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:38:03: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:38:03: #1 total tags in treatment: 1999207 INFO @ Sat, 08 Aug 2020 13:38:03: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:38:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:38:03: #1 tags after filtering in treatment: 1501759 INFO @ Sat, 08 Aug 2020 13:38:03: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 08 Aug 2020 13:38:03: #1 finished! INFO @ Sat, 08 Aug 2020 13:38:03: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:38:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:38:03: #2 number of paired peaks: 4 WARNING @ Sat, 08 Aug 2020 13:38:03: Too few paired peaks (4) 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, 08 Aug 2020 13:38:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX7917547/SRX7917547.20_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/SRX7917547/SRX7917547.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917547/SRX7917547.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917547/SRX7917547.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling