Job ID = 6528143 SRX = SRX474607 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T14:15:35 prefetch.2.10.7: 1) Downloading 'SRR1174460'... 2020-06-29T14:15:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:19:22 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:19:22 prefetch.2.10.7: 1) 'SRR1174460' was downloaded successfully 2020-06-29T14:19:22 prefetch.2.10.7: 'SRR1174460' has 0 unresolved dependencies Read 18331936 spots for SRR1174460/SRR1174460.sra Written 18331936 spots for SRR1174460/SRR1174460.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: 00:36:09 18331936 reads; of these: 18331936 (100.00%) were paired; of these: 1518675 (8.28%) aligned concordantly 0 times 11584651 (63.19%) aligned concordantly exactly 1 time 5228610 (28.52%) aligned concordantly >1 times ---- 1518675 pairs aligned concordantly 0 times; of these: 59496 (3.92%) aligned discordantly 1 time ---- 1459179 pairs aligned 0 times concordantly or discordantly; of these: 2918358 mates make up the pairs; of these: 2410372 (82.59%) aligned 0 times 335923 (11.51%) aligned exactly 1 time 172063 (5.90%) aligned >1 times 93.43% overall alignment rate Time searching: 00:36:09 Overall time: 00:36:09 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_sort_core] merging from 16 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] 2853480 / 16832684 = 0.1695 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 @ Tue, 30 Jun 2020 00:14:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474607/SRX474607.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474607/SRX474607.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474607/SRX474607.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474607/SRX474607.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 @ Tue, 30 Jun 2020 00:14:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:14:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:14:37: 1000000 INFO @ Tue, 30 Jun 2020 00:14:42: 2000000 INFO @ Tue, 30 Jun 2020 00:14:47: 3000000 INFO @ Tue, 30 Jun 2020 00:14:53: 4000000 INFO @ Tue, 30 Jun 2020 00:14:58: 5000000 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 @ Tue, 30 Jun 2020 00:15:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474607/SRX474607.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474607/SRX474607.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474607/SRX474607.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474607/SRX474607.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 @ Tue, 30 Jun 2020 00:15:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:15:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:15:03: 6000000 INFO @ Tue, 30 Jun 2020 00:15:07: 1000000 INFO @ Tue, 30 Jun 2020 00:15:09: 7000000 INFO @ Tue, 30 Jun 2020 00:15:13: 2000000 INFO @ Tue, 30 Jun 2020 00:15:15: 8000000 INFO @ Tue, 30 Jun 2020 00:15:19: 3000000 INFO @ Tue, 30 Jun 2020 00:15:21: 9000000 INFO @ Tue, 30 Jun 2020 00:15:25: 4000000 INFO @ Tue, 30 Jun 2020 00:15:26: 10000000 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 @ Tue, 30 Jun 2020 00:15:30: 5000000 INFO @ Tue, 30 Jun 2020 00:15:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474607/SRX474607.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474607/SRX474607.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474607/SRX474607.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474607/SRX474607.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 @ Tue, 30 Jun 2020 00:15:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:15:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:15:32: 11000000 INFO @ Tue, 30 Jun 2020 00:15:36: 6000000 INFO @ Tue, 30 Jun 2020 00:15:37: 1000000 INFO @ Tue, 30 Jun 2020 00:15:38: 12000000 INFO @ Tue, 30 Jun 2020 00:15:42: 7000000 INFO @ Tue, 30 Jun 2020 00:15:43: 2000000 INFO @ Tue, 30 Jun 2020 00:15:43: 13000000 INFO @ Tue, 30 Jun 2020 00:15:48: 8000000 INFO @ Tue, 30 Jun 2020 00:15:49: 3000000 INFO @ Tue, 30 Jun 2020 00:15:49: 14000000 INFO @ Tue, 30 Jun 2020 00:15:53: 9000000 INFO @ Tue, 30 Jun 2020 00:15:55: 4000000 INFO @ Tue, 30 Jun 2020 00:15:55: 15000000 INFO @ Tue, 30 Jun 2020 00:15:59: 10000000 INFO @ Tue, 30 Jun 2020 00:16:00: 5000000 INFO @ Tue, 30 Jun 2020 00:16:00: 16000000 INFO @ Tue, 30 Jun 2020 00:16:05: 11000000 INFO @ Tue, 30 Jun 2020 00:16:06: 6000000 INFO @ Tue, 30 Jun 2020 00:16:06: 17000000 INFO @ Tue, 30 Jun 2020 00:16:10: 12000000 INFO @ Tue, 30 Jun 2020 00:16:12: 7000000 INFO @ Tue, 30 Jun 2020 00:16:12: 18000000 INFO @ Tue, 30 Jun 2020 00:16:16: 13000000 INFO @ Tue, 30 Jun 2020 00:16:17: 8000000 INFO @ Tue, 30 Jun 2020 00:16:18: 19000000 INFO @ Tue, 30 Jun 2020 00:16:22: 14000000 INFO @ Tue, 30 Jun 2020 00:16:23: 9000000 INFO @ Tue, 30 Jun 2020 00:16:23: 20000000 INFO @ Tue, 30 Jun 2020 00:16:27: 15000000 INFO @ Tue, 30 Jun 2020 00:16:29: 10000000 INFO @ Tue, 30 Jun 2020 00:16:29: 21000000 INFO @ Tue, 30 Jun 2020 00:16:33: 16000000 INFO @ Tue, 30 Jun 2020 00:16:34: 11000000 INFO @ Tue, 30 Jun 2020 00:16:35: 22000000 INFO @ Tue, 30 Jun 2020 00:16:39: 17000000 INFO @ Tue, 30 Jun 2020 00:16:40: 12000000 INFO @ Tue, 30 Jun 2020 00:16:40: 23000000 INFO @ Tue, 30 Jun 2020 00:16:44: 18000000 INFO @ Tue, 30 Jun 2020 00:16:45: 24000000 INFO @ Tue, 30 Jun 2020 00:16:45: 13000000 INFO @ Tue, 30 Jun 2020 00:16:50: 19000000 INFO @ Tue, 30 Jun 2020 00:16:51: 25000000 INFO @ Tue, 30 Jun 2020 00:16:51: 14000000 INFO @ Tue, 30 Jun 2020 00:16:56: 20000000 INFO @ Tue, 30 Jun 2020 00:16:56: 26000000 INFO @ Tue, 30 Jun 2020 00:16:57: 15000000 INFO @ Tue, 30 Jun 2020 00:17:02: 21000000 INFO @ Tue, 30 Jun 2020 00:17:02: 27000000 INFO @ Tue, 30 Jun 2020 00:17:02: 16000000 INFO @ Tue, 30 Jun 2020 00:17:07: 22000000 INFO @ Tue, 30 Jun 2020 00:17:08: 28000000 INFO @ Tue, 30 Jun 2020 00:17:08: 17000000 INFO @ Tue, 30 Jun 2020 00:17:11: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:17:11: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:17:11: #1 total tags in treatment: 13962921 INFO @ Tue, 30 Jun 2020 00:17:11: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:17:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:17:11: #1 tags after filtering in treatment: 12260810 INFO @ Tue, 30 Jun 2020 00:17:11: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 30 Jun 2020 00:17:11: #1 finished! INFO @ Tue, 30 Jun 2020 00:17:11: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:17:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:17:12: #2 number of paired peaks: 74 WARNING @ Tue, 30 Jun 2020 00:17:12: Too few paired peaks (74) 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 @ Tue, 30 Jun 2020 00:17:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474607/SRX474607.05_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/SRX474607/SRX474607.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474607/SRX474607.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474607/SRX474607.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:17:13: 23000000 INFO @ Tue, 30 Jun 2020 00:17:13: 18000000 INFO @ Tue, 30 Jun 2020 00:17:18: 24000000 INFO @ Tue, 30 Jun 2020 00:17:19: 19000000 INFO @ Tue, 30 Jun 2020 00:17:24: 25000000 INFO @ Tue, 30 Jun 2020 00:17:24: 20000000 INFO @ Tue, 30 Jun 2020 00:17:29: 26000000 INFO @ Tue, 30 Jun 2020 00:17:30: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:17:35: 27000000 INFO @ Tue, 30 Jun 2020 00:17:36: 22000000 INFO @ Tue, 30 Jun 2020 00:17:40: 28000000 INFO @ Tue, 30 Jun 2020 00:17:41: 23000000 INFO @ Tue, 30 Jun 2020 00:17:44: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:17:44: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:17:44: #1 total tags in treatment: 13962921 INFO @ Tue, 30 Jun 2020 00:17:44: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:17:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:17:44: #1 tags after filtering in treatment: 12260810 INFO @ Tue, 30 Jun 2020 00:17:44: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 30 Jun 2020 00:17:44: #1 finished! INFO @ Tue, 30 Jun 2020 00:17:44: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:17:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:17:45: #2 number of paired peaks: 74 WARNING @ Tue, 30 Jun 2020 00:17:45: Too few paired peaks (74) 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 @ Tue, 30 Jun 2020 00:17:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474607/SRX474607.10_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/SRX474607/SRX474607.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474607/SRX474607.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474607/SRX474607.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:17:47: 24000000 INFO @ Tue, 30 Jun 2020 00:17:52: 25000000 INFO @ Tue, 30 Jun 2020 00:17:57: 26000000 INFO @ Tue, 30 Jun 2020 00:18:03: 27000000 INFO @ Tue, 30 Jun 2020 00:18:08: 28000000 INFO @ Tue, 30 Jun 2020 00:18:11: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:18:11: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:18:11: #1 total tags in treatment: 13962921 INFO @ Tue, 30 Jun 2020 00:18:11: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:18:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:18:11: #1 tags after filtering in treatment: 12260810 INFO @ Tue, 30 Jun 2020 00:18:11: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 30 Jun 2020 00:18:11: #1 finished! INFO @ Tue, 30 Jun 2020 00:18:11: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:18:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:18:12: #2 number of paired peaks: 74 WARNING @ Tue, 30 Jun 2020 00:18:12: Too few paired peaks (74) 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 @ Tue, 30 Jun 2020 00:18:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474607/SRX474607.20_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/SRX474607/SRX474607.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474607/SRX474607.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474607/SRX474607.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。