Job ID = 6527695 SRX = SRX2325640 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T13:38:28 prefetch.2.10.7: 1) Downloading 'SRR4896328'... 2020-06-29T13:38:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:42:25 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:42:25 prefetch.2.10.7: 1) 'SRR4896328' was downloaded successfully 2020-06-29T13:42:25 prefetch.2.10.7: 'SRR4896328' has 0 unresolved dependencies Read 23834444 spots for SRR4896328/SRR4896328.sra Written 23834444 spots for SRR4896328/SRR4896328.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: 00:45:56 23834444 reads; of these: 23834444 (100.00%) were paired; of these: 2545359 (10.68%) aligned concordantly 0 times 17408930 (73.04%) aligned concordantly exactly 1 time 3880155 (16.28%) aligned concordantly >1 times ---- 2545359 pairs aligned concordantly 0 times; of these: 513119 (20.16%) aligned discordantly 1 time ---- 2032240 pairs aligned 0 times concordantly or discordantly; of these: 4064480 mates make up the pairs; of these: 2560540 (63.00%) aligned 0 times 846749 (20.83%) aligned exactly 1 time 657191 (16.17%) aligned >1 times 94.63% overall alignment rate Time searching: 00:45:56 Overall time: 00:45:56 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 20 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] 876078 / 21639136 = 0.0405 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 00:01:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2325640/SRX2325640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2325640/SRX2325640.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2325640/SRX2325640.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2325640/SRX2325640.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 00:01:27: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:01:27: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:01:33: 1000000 INFO @ Tue, 30 Jun 2020 00:01:40: 2000000 INFO @ Tue, 30 Jun 2020 00:01:46: 3000000 INFO @ Tue, 30 Jun 2020 00:01:52: 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 @ Tue, 30 Jun 2020 00:01:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2325640/SRX2325640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2325640/SRX2325640.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2325640/SRX2325640.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2325640/SRX2325640.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 00:01:57: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:01:57: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:01:58: 5000000 INFO @ Tue, 30 Jun 2020 00:02:02: 1000000 INFO @ Tue, 30 Jun 2020 00:02:04: 6000000 INFO @ Tue, 30 Jun 2020 00:02:08: 2000000 INFO @ Tue, 30 Jun 2020 00:02:11: 7000000 INFO @ Tue, 30 Jun 2020 00:02:13: 3000000 INFO @ Tue, 30 Jun 2020 00:02:17: 8000000 INFO @ Tue, 30 Jun 2020 00:02:18: 4000000 INFO @ Tue, 30 Jun 2020 00:02:23: 9000000 INFO @ Tue, 30 Jun 2020 00:02:23: 5000000 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 00:02:28: 6000000 INFO @ Tue, 30 Jun 2020 00:02:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2325640/SRX2325640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2325640/SRX2325640.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2325640/SRX2325640.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2325640/SRX2325640.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 00:02:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:02:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:02:29: 10000000 INFO @ Tue, 30 Jun 2020 00:02:33: 7000000 INFO @ Tue, 30 Jun 2020 00:02:34: 1000000 INFO @ Tue, 30 Jun 2020 00:02:35: 11000000 INFO @ Tue, 30 Jun 2020 00:02:38: 8000000 INFO @ Tue, 30 Jun 2020 00:02:40: 2000000 INFO @ Tue, 30 Jun 2020 00:02:41: 12000000 INFO @ Tue, 30 Jun 2020 00:02:43: 9000000 INFO @ Tue, 30 Jun 2020 00:02:45: 3000000 INFO @ Tue, 30 Jun 2020 00:02:46: 13000000 INFO @ Tue, 30 Jun 2020 00:02:48: 10000000 INFO @ Tue, 30 Jun 2020 00:02:51: 4000000 INFO @ Tue, 30 Jun 2020 00:02:52: 14000000 INFO @ Tue, 30 Jun 2020 00:02:54: 11000000 INFO @ Tue, 30 Jun 2020 00:02:57: 5000000 INFO @ Tue, 30 Jun 2020 00:02:58: 15000000 INFO @ Tue, 30 Jun 2020 00:02:59: 12000000 INFO @ Tue, 30 Jun 2020 00:03:03: 6000000 INFO @ Tue, 30 Jun 2020 00:03:04: 13000000 INFO @ Tue, 30 Jun 2020 00:03:04: 16000000 INFO @ Tue, 30 Jun 2020 00:03:08: 7000000 INFO @ Tue, 30 Jun 2020 00:03:09: 14000000 INFO @ Tue, 30 Jun 2020 00:03:10: 17000000 INFO @ Tue, 30 Jun 2020 00:03:14: 15000000 INFO @ Tue, 30 Jun 2020 00:03:14: 8000000 INFO @ Tue, 30 Jun 2020 00:03:16: 18000000 INFO @ Tue, 30 Jun 2020 00:03:19: 16000000 INFO @ Tue, 30 Jun 2020 00:03:20: 9000000 INFO @ Tue, 30 Jun 2020 00:03:22: 19000000 INFO @ Tue, 30 Jun 2020 00:03:24: 17000000 INFO @ Tue, 30 Jun 2020 00:03:26: 10000000 INFO @ Tue, 30 Jun 2020 00:03:28: 20000000 INFO @ Tue, 30 Jun 2020 00:03:29: 18000000 INFO @ Tue, 30 Jun 2020 00:03:31: 11000000 INFO @ Tue, 30 Jun 2020 00:03:34: 19000000 INFO @ Tue, 30 Jun 2020 00:03:34: 21000000 INFO @ Tue, 30 Jun 2020 00:03:37: 12000000 INFO @ Tue, 30 Jun 2020 00:03:39: 20000000 INFO @ Tue, 30 Jun 2020 00:03:40: 22000000 INFO @ Tue, 30 Jun 2020 00:03:43: 13000000 INFO @ Tue, 30 Jun 2020 00:03:44: 21000000 INFO @ Tue, 30 Jun 2020 00:03:46: 23000000 INFO @ Tue, 30 Jun 2020 00:03:49: 14000000 INFO @ Tue, 30 Jun 2020 00:03:49: 22000000 INFO @ Tue, 30 Jun 2020 00:03:52: 24000000 INFO @ Tue, 30 Jun 2020 00:03:54: 23000000 INFO @ Tue, 30 Jun 2020 00:03:55: 15000000 INFO @ Tue, 30 Jun 2020 00:03:58: 25000000 INFO @ Tue, 30 Jun 2020 00:03:59: 24000000 INFO @ Tue, 30 Jun 2020 00:04:01: 16000000 INFO @ Tue, 30 Jun 2020 00:04:04: 25000000 INFO @ Tue, 30 Jun 2020 00:04:04: 26000000 INFO @ Tue, 30 Jun 2020 00:04:07: 17000000 INFO @ Tue, 30 Jun 2020 00:04:09: 26000000 INFO @ Tue, 30 Jun 2020 00:04:10: 27000000 INFO @ Tue, 30 Jun 2020 00:04:13: 18000000 INFO @ Tue, 30 Jun 2020 00:04:14: 27000000 INFO @ Tue, 30 Jun 2020 00:04:16: 28000000 INFO @ Tue, 30 Jun 2020 00:04:19: 19000000 INFO @ Tue, 30 Jun 2020 00:04:19: 28000000 INFO @ Tue, 30 Jun 2020 00:04:22: 29000000 INFO @ Tue, 30 Jun 2020 00:04:24: 29000000 INFO @ Tue, 30 Jun 2020 00:04:25: 20000000 INFO @ Tue, 30 Jun 2020 00:04:29: 30000000 INFO @ Tue, 30 Jun 2020 00:04:29: 30000000 INFO @ Tue, 30 Jun 2020 00:04:31: 21000000 INFO @ Tue, 30 Jun 2020 00:04:35: 31000000 INFO @ Tue, 30 Jun 2020 00:04:35: 31000000 INFO @ Tue, 30 Jun 2020 00:04:36: 22000000 INFO @ Tue, 30 Jun 2020 00:04:41: 32000000 INFO @ Tue, 30 Jun 2020 00:04:42: 32000000 INFO @ Tue, 30 Jun 2020 00:04:42: 23000000 INFO @ Tue, 30 Jun 2020 00:04:47: 33000000 INFO @ Tue, 30 Jun 2020 00:04:48: 33000000 INFO @ Tue, 30 Jun 2020 00:04:48: 24000000 INFO @ Tue, 30 Jun 2020 00:04:53: 34000000 INFO @ Tue, 30 Jun 2020 00:04:54: 34000000 INFO @ Tue, 30 Jun 2020 00:04:54: 25000000 INFO @ Tue, 30 Jun 2020 00:04:59: 35000000 INFO @ Tue, 30 Jun 2020 00:05:00: 35000000 INFO @ Tue, 30 Jun 2020 00:05:00: 26000000 INFO @ Tue, 30 Jun 2020 00:05:06: 36000000 INFO @ Tue, 30 Jun 2020 00:05:06: 27000000 INFO @ Tue, 30 Jun 2020 00:05:06: 36000000 INFO @ Tue, 30 Jun 2020 00:05:12: 28000000 INFO @ Tue, 30 Jun 2020 00:05:12: 37000000 INFO @ Tue, 30 Jun 2020 00:05:12: 37000000 INFO @ Tue, 30 Jun 2020 00:05:18: 29000000 INFO @ Tue, 30 Jun 2020 00:05:18: 38000000 INFO @ Tue, 30 Jun 2020 00:05:19: 38000000 INFO @ Tue, 30 Jun 2020 00:05:24: 30000000 INFO @ Tue, 30 Jun 2020 00:05:25: 39000000 INFO @ Tue, 30 Jun 2020 00:05:25: 39000000 INFO @ Tue, 30 Jun 2020 00:05:30: 31000000 INFO @ Tue, 30 Jun 2020 00:05:31: 40000000 INFO @ Tue, 30 Jun 2020 00:05:31: 40000000 INFO @ Tue, 30 Jun 2020 00:05:36: 32000000 INFO @ Tue, 30 Jun 2020 00:05:37: 41000000 INFO @ Tue, 30 Jun 2020 00:05:38: 41000000 INFO @ Tue, 30 Jun 2020 00:05:42: 33000000 INFO @ Tue, 30 Jun 2020 00:05:44: 42000000 INFO @ Tue, 30 Jun 2020 00:05:44: 42000000 INFO @ Tue, 30 Jun 2020 00:05:48: 34000000 INFO @ Tue, 30 Jun 2020 00:05:50: 43000000 INFO @ Tue, 30 Jun 2020 00:05:50: 43000000 INFO @ Tue, 30 Jun 2020 00:05:52: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 00:05:52: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 00:05:52: #1 total tags in treatment: 20421126 INFO @ Tue, 30 Jun 2020 00:05:52: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:05:52: #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 00:05:52: #1 tags after filtering in treatment: 18906221 INFO @ Tue, 30 Jun 2020 00:05:52: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 30 Jun 2020 00:05:52: #1 finished! INFO @ Tue, 30 Jun 2020 00:05:52: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:05:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:05:53: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 00:05:53: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 00:05:53: #1 total tags in treatment: 20421126 INFO @ Tue, 30 Jun 2020 00:05:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:05:53: #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 00:05:53: #1 tags after filtering in treatment: 18906221 INFO @ Tue, 30 Jun 2020 00:05:53: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 30 Jun 2020 00:05:53: #1 finished! INFO @ Tue, 30 Jun 2020 00:05:53: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:05:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:05:54: 35000000 INFO @ Tue, 30 Jun 2020 00:05:54: #2 number of paired peaks: 43 WARNING @ Tue, 30 Jun 2020 00:05:54: Too few paired peaks (43) 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 00:05:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX2325640/SRX2325640.05_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/SRX2325640/SRX2325640.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2325640/SRX2325640.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2325640/SRX2325640.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:05:54: #2 number of paired peaks: 43 WARNING @ Tue, 30 Jun 2020 00:05:54: Too few paired peaks (43) 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 00:05:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX2325640/SRX2325640.10_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/SRX2325640/SRX2325640.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2325640/SRX2325640.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2325640/SRX2325640.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:06:00: 36000000 INFO @ Tue, 30 Jun 2020 00:06:06: 37000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:06:12: 38000000 INFO @ Tue, 30 Jun 2020 00:06:18: 39000000 INFO @ Tue, 30 Jun 2020 00:06:24: 40000000 INFO @ Tue, 30 Jun 2020 00:06:29: 41000000 INFO @ Tue, 30 Jun 2020 00:06:35: 42000000 INFO @ Tue, 30 Jun 2020 00:06:41: 43000000 INFO @ Tue, 30 Jun 2020 00:06:43: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 00:06:43: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 00:06:43: #1 total tags in treatment: 20421126 INFO @ Tue, 30 Jun 2020 00:06:43: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:06:43: #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 00:06:44: #1 tags after filtering in treatment: 18906221 INFO @ Tue, 30 Jun 2020 00:06:44: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 30 Jun 2020 00:06:44: #1 finished! INFO @ Tue, 30 Jun 2020 00:06:44: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:06:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:06:45: #2 number of paired peaks: 43 WARNING @ Tue, 30 Jun 2020 00:06:45: Too few paired peaks (43) 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 00:06:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX2325640/SRX2325640.20_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/SRX2325640/SRX2325640.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2325640/SRX2325640.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2325640/SRX2325640.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。