Job ID = 8070997 SRX = SRX7917499 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T04:17:08 prefetch.2.10.7: 1) Downloading 'SRR11313080'... 2020-08-08T04:17:08 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T04:17:40 prefetch.2.10.7: HTTPS download succeed 2020-08-08T04:17:41 prefetch.2.10.7: 'SRR11313080' is valid 2020-08-08T04:17:41 prefetch.2.10.7: 1) 'SRR11313080' was downloaded successfully Read 3774551 spots for SRR11313080/SRR11313080.sra Written 3774551 spots for SRR11313080/SRR11313080.sra fastq に変換しました。 bowtie でマッピング中... Your job 8072098 ("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: 00:07:07 3774551 reads; of these: 3774551 (100.00%) were paired; of these: 659943 (17.48%) aligned concordantly 0 times 2369602 (62.78%) aligned concordantly exactly 1 time 745006 (19.74%) aligned concordantly >1 times ---- 659943 pairs aligned concordantly 0 times; of these: 213981 (32.42%) aligned discordantly 1 time ---- 445962 pairs aligned 0 times concordantly or discordantly; of these: 891924 mates make up the pairs; of these: 559989 (62.78%) aligned 0 times 160707 (18.02%) aligned exactly 1 time 171228 (19.20%) aligned >1 times 92.58% overall alignment rate Time searching: 00:07:07 Overall time: 00:07:07 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 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] 1136590 / 3315871 = 0.3428 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 13:26:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917499/SRX7917499.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917499/SRX7917499.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917499/SRX7917499.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917499/SRX7917499.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 13:26:58: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:26:58: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:27:03: 1000000 INFO @ Sat, 08 Aug 2020 13:27:09: 2000000 INFO @ Sat, 08 Aug 2020 13:27:14: 3000000 INFO @ Sat, 08 Aug 2020 13:27:20: 4000000 INFO @ Sat, 08 Aug 2020 13:27:23: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:27:23: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:27:23: #1 total tags in treatment: 1994578 INFO @ Sat, 08 Aug 2020 13:27:23: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:27:23: #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 13:27:23: #1 tags after filtering in treatment: 1507305 INFO @ Sat, 08 Aug 2020 13:27:23: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 08 Aug 2020 13:27:23: #1 finished! INFO @ Sat, 08 Aug 2020 13:27:23: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:27:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:27:24: #2 number of paired peaks: 7 WARNING @ Sat, 08 Aug 2020 13:27:24: Too few paired peaks (7) 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 13:27:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX7917499/SRX7917499.05_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/SRX7917499/SRX7917499.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917499/SRX7917499.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917499/SRX7917499.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 13:27:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917499/SRX7917499.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917499/SRX7917499.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917499/SRX7917499.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917499/SRX7917499.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 13:27:28: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:27:28: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:27:34: 1000000 INFO @ Sat, 08 Aug 2020 13:27:41: 2000000 INFO @ Sat, 08 Aug 2020 13:27:48: 3000000 INFO @ Sat, 08 Aug 2020 13:27:55: 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 13:27:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917499/SRX7917499.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917499/SRX7917499.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917499/SRX7917499.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917499/SRX7917499.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 13:27:58: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:27:58: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:28:00: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:28:00: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:28:00: #1 total tags in treatment: 1994578 INFO @ Sat, 08 Aug 2020 13:28:00: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:28:00: #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 13:28:00: #1 tags after filtering in treatment: 1507305 INFO @ Sat, 08 Aug 2020 13:28:00: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 08 Aug 2020 13:28:00: #1 finished! INFO @ Sat, 08 Aug 2020 13:28:00: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:28:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:28:01: #2 number of paired peaks: 7 WARNING @ Sat, 08 Aug 2020 13:28:01: Too few paired peaks (7) 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 13:28:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX7917499/SRX7917499.10_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/dm3/SRX7917499/SRX7917499.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917499/SRX7917499.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917499/SRX7917499.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:28:04: 1000000 INFO @ Sat, 08 Aug 2020 13:28:09: 2000000 INFO @ Sat, 08 Aug 2020 13:28:15: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:28:21: 4000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:28:24: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:28:24: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:28:24: #1 total tags in treatment: 1994578 INFO @ Sat, 08 Aug 2020 13:28:24: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:28:24: #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 13:28:24: #1 tags after filtering in treatment: 1507305 INFO @ Sat, 08 Aug 2020 13:28:24: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 08 Aug 2020 13:28:24: #1 finished! INFO @ Sat, 08 Aug 2020 13:28:24: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:28:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:28:25: #2 number of paired peaks: 7 WARNING @ Sat, 08 Aug 2020 13:28:25: Too few paired peaks (7) 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 13:28:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX7917499/SRX7917499.20_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/SRX7917499/SRX7917499.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917499/SRX7917499.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917499/SRX7917499.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling