Job ID = 8069872 SRX = SRX7917475 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:57:24 prefetch.2.10.7: 1) Downloading 'SRR11313056'... 2020-08-08T03:57:24 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:58:03 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:58:03 prefetch.2.10.7: 'SRR11313056' is valid 2020-08-08T03:58:03 prefetch.2.10.7: 1) 'SRR11313056' was downloaded successfully Read 4213859 spots for SRR11313056/SRR11313056.sra Written 4213859 spots for SRR11313056/SRR11313056.sra fastq に変換しました。 bowtie でマッピング中... Your job 8071112 ("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: 00:06:16 4213859 reads; of these: 4213859 (100.00%) were paired; of these: 1512882 (35.90%) aligned concordantly 0 times 2057788 (48.83%) aligned concordantly exactly 1 time 643189 (15.26%) aligned concordantly >1 times ---- 1512882 pairs aligned concordantly 0 times; of these: 184601 (12.20%) aligned discordantly 1 time ---- 1328281 pairs aligned 0 times concordantly or discordantly; of these: 2656562 mates make up the pairs; of these: 2371126 (89.26%) aligned 0 times 139754 (5.26%) aligned exactly 1 time 145682 (5.48%) aligned >1 times 71.87% overall alignment rate Time searching: 00:06:16 Overall time: 00:06:16 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] 963286 / 2874050 = 0.3352 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 13:06:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917475/SRX7917475.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917475/SRX7917475.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917475/SRX7917475.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917475/SRX7917475.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 13:06:25: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:06:25: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:06:32: 1000000 INFO @ Sat, 08 Aug 2020 13:06:39: 2000000 INFO @ Sat, 08 Aug 2020 13:06:46: 3000000 INFO @ Sat, 08 Aug 2020 13:06:51: 4000000 INFO @ Sat, 08 Aug 2020 13:06:52: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:06:52: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:06:52: #1 total tags in treatment: 1751550 INFO @ Sat, 08 Aug 2020 13:06:52: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:06:52: #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 13:06:52: #1 tags after filtering in treatment: 1360510 INFO @ Sat, 08 Aug 2020 13:06:52: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 08 Aug 2020 13:06:52: #1 finished! INFO @ Sat, 08 Aug 2020 13:06:52: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:06:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:06:52: #2 number of paired peaks: 7 WARNING @ Sat, 08 Aug 2020 13:06:52: 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 13:06:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX7917475/SRX7917475.05_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/dm3/SRX7917475/SRX7917475.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917475/SRX7917475.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917475/SRX7917475.05_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 13:06:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917475/SRX7917475.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917475/SRX7917475.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917475/SRX7917475.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917475/SRX7917475.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 13:06:55: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:06:55: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:07:00: 1000000 INFO @ Sat, 08 Aug 2020 13:07:06: 2000000 INFO @ Sat, 08 Aug 2020 13:07:11: 3000000 INFO @ Sat, 08 Aug 2020 13:07:17: 4000000 INFO @ Sat, 08 Aug 2020 13:07:17: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:07:17: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:07:17: #1 total tags in treatment: 1751550 INFO @ Sat, 08 Aug 2020 13:07:17: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:07:17: #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 13:07:17: #1 tags after filtering in treatment: 1360510 INFO @ Sat, 08 Aug 2020 13:07:17: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 08 Aug 2020 13:07:17: #1 finished! INFO @ Sat, 08 Aug 2020 13:07:17: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:07:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:07:17: #2 number of paired peaks: 7 WARNING @ Sat, 08 Aug 2020 13:07:17: 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 13:07:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX7917475/SRX7917475.10_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/SRX7917475/SRX7917475.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917475/SRX7917475.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917475/SRX7917475.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 13:07:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917475/SRX7917475.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917475/SRX7917475.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917475/SRX7917475.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917475/SRX7917475.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 13:07:25: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:07:25: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:07:31: 1000000 INFO @ Sat, 08 Aug 2020 13:07:36: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:07:42: 3000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:07:48: 4000000 INFO @ Sat, 08 Aug 2020 13:07:49: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:07:49: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:07:49: #1 total tags in treatment: 1751550 INFO @ Sat, 08 Aug 2020 13:07:49: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:07:49: #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 13:07:49: #1 tags after filtering in treatment: 1360510 INFO @ Sat, 08 Aug 2020 13:07:49: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 08 Aug 2020 13:07:49: #1 finished! INFO @ Sat, 08 Aug 2020 13:07:49: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:07:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:07:49: #2 number of paired peaks: 7 WARNING @ Sat, 08 Aug 2020 13:07:49: 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 13:07:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX7917475/SRX7917475.20_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/SRX7917475/SRX7917475.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917475/SRX7917475.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7917475/SRX7917475.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling