Job ID = 14172378 SRX = SRX5681716 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-11T06:11:51 fastq-dump.2.10.7 err: data corrupt while executing function within transform module - failed SRR8895593/SRR8895593.sra ============================================================= An error occurred during processing. A report was generated into the file '/home/okishinya/ncbi_error_report.txt'. If the problem persists, you may consider sending the file to 'sra-tools@ncbi.nlm.nih.gov' for assistance. ============================================================= fastq-dump quit with error code 3 Read 8702322 spots for SRR8895594/SRR8895594.sra Written 8702322 spots for SRR8895594/SRR8895594.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172904 ("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: 00:23:41 11568338 reads; of these: 11568338 (100.00%) were paired; of these: 1292693 (11.17%) aligned concordantly 0 times 8521457 (73.66%) aligned concordantly exactly 1 time 1754188 (15.16%) aligned concordantly >1 times ---- 1292693 pairs aligned concordantly 0 times; of these: 550578 (42.59%) aligned discordantly 1 time ---- 742115 pairs aligned 0 times concordantly or discordantly; of these: 1484230 mates make up the pairs; of these: 958679 (64.59%) aligned 0 times 269547 (18.16%) aligned exactly 1 time 256004 (17.25%) aligned >1 times 95.86% overall alignment rate Time searching: 00:23:41 Overall time: 00:23:41 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_sort_core] merging from 12 files... [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] 453786 / 10764371 = 0.0422 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, 11 Dec 2021 15:43:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5681716/SRX5681716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5681716/SRX5681716.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5681716/SRX5681716.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5681716/SRX5681716.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, 11 Dec 2021 15:43:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:43:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:43:47: 1000000 INFO @ Sat, 11 Dec 2021 15:43:53: 2000000 INFO @ Sat, 11 Dec 2021 15:43:58: 3000000 INFO @ Sat, 11 Dec 2021 15:44:04: 4000000 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, 11 Dec 2021 15:44:10: 5000000 INFO @ Sat, 11 Dec 2021 15:44:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5681716/SRX5681716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5681716/SRX5681716.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5681716/SRX5681716.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5681716/SRX5681716.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, 11 Dec 2021 15:44:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:44:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:44:16: 6000000 INFO @ Sat, 11 Dec 2021 15:44:17: 1000000 INFO @ Sat, 11 Dec 2021 15:44:22: 7000000 INFO @ Sat, 11 Dec 2021 15:44:24: 2000000 INFO @ Sat, 11 Dec 2021 15:44:29: 8000000 INFO @ Sat, 11 Dec 2021 15:44:30: 3000000 INFO @ Sat, 11 Dec 2021 15:44:35: 9000000 INFO @ Sat, 11 Dec 2021 15:44:37: 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, 11 Dec 2021 15:44:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5681716/SRX5681716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5681716/SRX5681716.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5681716/SRX5681716.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5681716/SRX5681716.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, 11 Dec 2021 15:44:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:44:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:44:41: 10000000 INFO @ Sat, 11 Dec 2021 15:44:43: 5000000 INFO @ Sat, 11 Dec 2021 15:44:47: 1000000 INFO @ Sat, 11 Dec 2021 15:44:47: 11000000 INFO @ Sat, 11 Dec 2021 15:44:50: 6000000 INFO @ Sat, 11 Dec 2021 15:44:54: 2000000 INFO @ Sat, 11 Dec 2021 15:44:54: 12000000 INFO @ Sat, 11 Dec 2021 15:44:56: 7000000 INFO @ Sat, 11 Dec 2021 15:45:00: 3000000 INFO @ Sat, 11 Dec 2021 15:45:00: 13000000 INFO @ Sat, 11 Dec 2021 15:45:02: 8000000 INFO @ Sat, 11 Dec 2021 15:45:06: 4000000 INFO @ Sat, 11 Dec 2021 15:45:06: 14000000 INFO @ Sat, 11 Dec 2021 15:45:09: 9000000 INFO @ Sat, 11 Dec 2021 15:45:12: 5000000 INFO @ Sat, 11 Dec 2021 15:45:12: 15000000 INFO @ Sat, 11 Dec 2021 15:45:15: 10000000 INFO @ Sat, 11 Dec 2021 15:45:18: 16000000 INFO @ Sat, 11 Dec 2021 15:45:18: 6000000 INFO @ Sat, 11 Dec 2021 15:45:22: 11000000 INFO @ Sat, 11 Dec 2021 15:45:25: 17000000 INFO @ Sat, 11 Dec 2021 15:45:25: 7000000 INFO @ Sat, 11 Dec 2021 15:45:28: 12000000 INFO @ Sat, 11 Dec 2021 15:45:31: 18000000 INFO @ Sat, 11 Dec 2021 15:45:31: 8000000 INFO @ Sat, 11 Dec 2021 15:45:35: 13000000 INFO @ Sat, 11 Dec 2021 15:45:38: 9000000 INFO @ Sat, 11 Dec 2021 15:45:38: 19000000 INFO @ Sat, 11 Dec 2021 15:45:41: 14000000 INFO @ Sat, 11 Dec 2021 15:45:44: 10000000 INFO @ Sat, 11 Dec 2021 15:45:44: 20000000 INFO @ Sat, 11 Dec 2021 15:45:47: 15000000 INFO @ Sat, 11 Dec 2021 15:45:50: 11000000 INFO @ Sat, 11 Dec 2021 15:45:50: 21000000 INFO @ Sat, 11 Dec 2021 15:45:52: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 15:45:52: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 15:45:52: #1 total tags in treatment: 9838690 INFO @ Sat, 11 Dec 2021 15:45:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:45:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:45:52: #1 tags after filtering in treatment: 9039969 INFO @ Sat, 11 Dec 2021 15:45:52: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 15:45:52: #1 finished! INFO @ Sat, 11 Dec 2021 15:45:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:45:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:45:53: #2 number of paired peaks: 12 WARNING @ Sat, 11 Dec 2021 15:45:53: Too few paired peaks (12) 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, 11 Dec 2021 15:45:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5681716/SRX5681716.05_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/SRX5681716/SRX5681716.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5681716/SRX5681716.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5681716/SRX5681716.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:45:54: 16000000 INFO @ Sat, 11 Dec 2021 15:45:56: 12000000 INFO @ Sat, 11 Dec 2021 15:46:00: 17000000 INFO @ Sat, 11 Dec 2021 15:46:02: 13000000 INFO @ Sat, 11 Dec 2021 15:46:06: 18000000 INFO @ Sat, 11 Dec 2021 15:46:08: 14000000 INFO @ Sat, 11 Dec 2021 15:46:13: 19000000 INFO @ Sat, 11 Dec 2021 15:46:14: 15000000 INFO @ Sat, 11 Dec 2021 15:46:19: 20000000 INFO @ Sat, 11 Dec 2021 15:46:20: 16000000 INFO @ Sat, 11 Dec 2021 15:46:25: 21000000 INFO @ Sat, 11 Dec 2021 15:46:26: 17000000 INFO @ Sat, 11 Dec 2021 15:46:27: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 15:46:27: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 15:46:27: #1 total tags in treatment: 9838690 INFO @ Sat, 11 Dec 2021 15:46:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:46:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:46:27: #1 tags after filtering in treatment: 9039969 INFO @ Sat, 11 Dec 2021 15:46:27: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 15:46:27: #1 finished! INFO @ Sat, 11 Dec 2021 15:46:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:46:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:46:28: #2 number of paired peaks: 12 WARNING @ Sat, 11 Dec 2021 15:46:28: Too few paired peaks (12) 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, 11 Dec 2021 15:46:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5681716/SRX5681716.10_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/SRX5681716/SRX5681716.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5681716/SRX5681716.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5681716/SRX5681716.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:46:32: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:46:38: 19000000 INFO @ Sat, 11 Dec 2021 15:46:44: 20000000 INFO @ Sat, 11 Dec 2021 15:46:50: 21000000 INFO @ Sat, 11 Dec 2021 15:46:52: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 15:46:52: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 15:46:52: #1 total tags in treatment: 9838690 INFO @ Sat, 11 Dec 2021 15:46:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:46:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:46:52: #1 tags after filtering in treatment: 9039969 INFO @ Sat, 11 Dec 2021 15:46:52: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 15:46:52: #1 finished! INFO @ Sat, 11 Dec 2021 15:46:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:46:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:46:53: #2 number of paired peaks: 12 WARNING @ Sat, 11 Dec 2021 15:46:53: Too few paired peaks (12) 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, 11 Dec 2021 15:46:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5681716/SRX5681716.20_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/SRX5681716/SRX5681716.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5681716/SRX5681716.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5681716/SRX5681716.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。