Job ID = 6527902 SRX = SRX3159484 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:13:06 prefetch.2.10.7: 1) Downloading 'SRR6004214'... 2020-06-29T14:13:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:15:30 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:15:30 prefetch.2.10.7: 1) 'SRR6004214' was downloaded successfully 2020-06-29T14:15:30 prefetch.2.10.7: 'SRR6004214' has 0 unresolved dependencies Read 42389119 spots for SRR6004214/SRR6004214.sra Written 42389119 spots for SRR6004214/SRR6004214.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: 00:17:46 42389119 reads; of these: 42389119 (100.00%) were unpaired; of these: 818693 (1.93%) aligned 0 times 29011380 (68.44%) aligned exactly 1 time 12559046 (29.63%) aligned >1 times 98.07% overall alignment rate Time searching: 00:17:46 Overall time: 00:17:46 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_rmdupse_core] 6706931 / 41570426 = 0.1613 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 @ Mon, 29 Jun 2020 23:57:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3159484/SRX3159484.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3159484/SRX3159484.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3159484/SRX3159484.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3159484/SRX3159484.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 @ Mon, 29 Jun 2020 23:57:34: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:57:34: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:57:41: 1000000 INFO @ Mon, 29 Jun 2020 23:57:48: 2000000 INFO @ Mon, 29 Jun 2020 23:57:54: 3000000 INFO @ Mon, 29 Jun 2020 23:58:00: 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 @ Mon, 29 Jun 2020 23:58:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3159484/SRX3159484.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3159484/SRX3159484.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3159484/SRX3159484.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3159484/SRX3159484.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 @ Mon, 29 Jun 2020 23:58:04: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:58:04: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:58:07: 5000000 INFO @ Mon, 29 Jun 2020 23:58:12: 1000000 INFO @ Mon, 29 Jun 2020 23:58:14: 6000000 INFO @ Mon, 29 Jun 2020 23:58:19: 2000000 INFO @ Mon, 29 Jun 2020 23:58:21: 7000000 INFO @ Mon, 29 Jun 2020 23:58:27: 3000000 INFO @ Mon, 29 Jun 2020 23:58:29: 8000000 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 @ Mon, 29 Jun 2020 23:58:34: 4000000 INFO @ Mon, 29 Jun 2020 23:58:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3159484/SRX3159484.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3159484/SRX3159484.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3159484/SRX3159484.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3159484/SRX3159484.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 @ Mon, 29 Jun 2020 23:58:34: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:58:34: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:58:36: 9000000 INFO @ Mon, 29 Jun 2020 23:58:42: 5000000 INFO @ Mon, 29 Jun 2020 23:58:42: 1000000 INFO @ Mon, 29 Jun 2020 23:58:44: 10000000 INFO @ Mon, 29 Jun 2020 23:58:50: 6000000 INFO @ Mon, 29 Jun 2020 23:58:51: 2000000 INFO @ Mon, 29 Jun 2020 23:58:52: 11000000 INFO @ Mon, 29 Jun 2020 23:58:58: 7000000 INFO @ Mon, 29 Jun 2020 23:58:59: 3000000 INFO @ Mon, 29 Jun 2020 23:59:00: 12000000 INFO @ Mon, 29 Jun 2020 23:59:06: 8000000 INFO @ Mon, 29 Jun 2020 23:59:06: 4000000 INFO @ Mon, 29 Jun 2020 23:59:08: 13000000 INFO @ Mon, 29 Jun 2020 23:59:14: 9000000 INFO @ Mon, 29 Jun 2020 23:59:14: 5000000 INFO @ Mon, 29 Jun 2020 23:59:16: 14000000 INFO @ Mon, 29 Jun 2020 23:59:21: 10000000 INFO @ Mon, 29 Jun 2020 23:59:22: 6000000 INFO @ Mon, 29 Jun 2020 23:59:24: 15000000 INFO @ Mon, 29 Jun 2020 23:59:29: 11000000 INFO @ Mon, 29 Jun 2020 23:59:30: 7000000 INFO @ Mon, 29 Jun 2020 23:59:32: 16000000 INFO @ Mon, 29 Jun 2020 23:59:37: 12000000 INFO @ Mon, 29 Jun 2020 23:59:38: 8000000 INFO @ Mon, 29 Jun 2020 23:59:40: 17000000 INFO @ Mon, 29 Jun 2020 23:59:45: 13000000 INFO @ Mon, 29 Jun 2020 23:59:46: 9000000 INFO @ Mon, 29 Jun 2020 23:59:47: 18000000 INFO @ Mon, 29 Jun 2020 23:59:53: 14000000 INFO @ Mon, 29 Jun 2020 23:59:53: 10000000 INFO @ Mon, 29 Jun 2020 23:59:55: 19000000 INFO @ Tue, 30 Jun 2020 00:00:01: 11000000 INFO @ Tue, 30 Jun 2020 00:00:01: 15000000 INFO @ Tue, 30 Jun 2020 00:00:03: 20000000 INFO @ Tue, 30 Jun 2020 00:00:09: 12000000 INFO @ Tue, 30 Jun 2020 00:00:09: 16000000 INFO @ Tue, 30 Jun 2020 00:00:11: 21000000 INFO @ Tue, 30 Jun 2020 00:00:17: 13000000 INFO @ Tue, 30 Jun 2020 00:00:17: 17000000 INFO @ Tue, 30 Jun 2020 00:00:19: 22000000 INFO @ Tue, 30 Jun 2020 00:00:24: 14000000 INFO @ Tue, 30 Jun 2020 00:00:25: 18000000 INFO @ Tue, 30 Jun 2020 00:00:27: 23000000 INFO @ Tue, 30 Jun 2020 00:00:33: 19000000 INFO @ Tue, 30 Jun 2020 00:00:33: 15000000 INFO @ Tue, 30 Jun 2020 00:00:35: 24000000 INFO @ Tue, 30 Jun 2020 00:00:41: 16000000 INFO @ Tue, 30 Jun 2020 00:00:41: 20000000 INFO @ Tue, 30 Jun 2020 00:00:44: 25000000 INFO @ Tue, 30 Jun 2020 00:00:49: 17000000 INFO @ Tue, 30 Jun 2020 00:00:50: 21000000 INFO @ Tue, 30 Jun 2020 00:00:52: 26000000 INFO @ Tue, 30 Jun 2020 00:00:57: 18000000 INFO @ Tue, 30 Jun 2020 00:00:58: 22000000 INFO @ Tue, 30 Jun 2020 00:01:00: 27000000 INFO @ Tue, 30 Jun 2020 00:01:05: 19000000 INFO @ Tue, 30 Jun 2020 00:01:07: 23000000 INFO @ Tue, 30 Jun 2020 00:01:09: 28000000 INFO @ Tue, 30 Jun 2020 00:01:13: 20000000 INFO @ Tue, 30 Jun 2020 00:01:15: 24000000 INFO @ Tue, 30 Jun 2020 00:01:18: 29000000 INFO @ Tue, 30 Jun 2020 00:01:22: 21000000 INFO @ Tue, 30 Jun 2020 00:01:24: 25000000 INFO @ Tue, 30 Jun 2020 00:01:26: 30000000 INFO @ Tue, 30 Jun 2020 00:01:30: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:01:32: 26000000 INFO @ Tue, 30 Jun 2020 00:01:35: 31000000 INFO @ Tue, 30 Jun 2020 00:01:39: 23000000 INFO @ Tue, 30 Jun 2020 00:01:41: 27000000 INFO @ Tue, 30 Jun 2020 00:01:43: 32000000 INFO @ Tue, 30 Jun 2020 00:01:47: 24000000 INFO @ Tue, 30 Jun 2020 00:01:50: 28000000 INFO @ Tue, 30 Jun 2020 00:01:52: 33000000 INFO @ Tue, 30 Jun 2020 00:01:56: 25000000 INFO @ Tue, 30 Jun 2020 00:01:58: 29000000 INFO @ Tue, 30 Jun 2020 00:02:00: 34000000 INFO @ Tue, 30 Jun 2020 00:02:04: 26000000 INFO @ Tue, 30 Jun 2020 00:02:06: 30000000 INFO @ Tue, 30 Jun 2020 00:02:07: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 00:02:07: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 00:02:07: #1 total tags in treatment: 34863495 INFO @ Tue, 30 Jun 2020 00:02:07: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:02:07: #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 00:02:08: #1 tags after filtering in treatment: 34863495 INFO @ Tue, 30 Jun 2020 00:02:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:02:08: #1 finished! INFO @ Tue, 30 Jun 2020 00:02:08: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:02:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:02:10: #2 number of paired peaks: 8 WARNING @ Tue, 30 Jun 2020 00:02:10: Too few paired peaks (8) 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 00:02:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3159484/SRX3159484.05_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/SRX3159484/SRX3159484.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3159484/SRX3159484.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3159484/SRX3159484.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:02:13: 27000000 INFO @ Tue, 30 Jun 2020 00:02:15: 31000000 INFO @ Tue, 30 Jun 2020 00:02:21: 28000000 INFO @ Tue, 30 Jun 2020 00:02:23: 32000000 INFO @ Tue, 30 Jun 2020 00:02:30: 29000000 INFO @ Tue, 30 Jun 2020 00:02:31: 33000000 INFO @ Tue, 30 Jun 2020 00:02:38: 30000000 INFO @ Tue, 30 Jun 2020 00:02:40: 34000000 INFO @ Tue, 30 Jun 2020 00:02:47: 31000000 INFO @ Tue, 30 Jun 2020 00:02:47: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 00:02:47: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 00:02:47: #1 total tags in treatment: 34863495 INFO @ Tue, 30 Jun 2020 00:02:47: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:02:47: #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 00:02:48: #1 tags after filtering in treatment: 34863495 INFO @ Tue, 30 Jun 2020 00:02:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:02:48: #1 finished! INFO @ Tue, 30 Jun 2020 00:02:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:02:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:02:50: #2 number of paired peaks: 8 WARNING @ Tue, 30 Jun 2020 00:02:50: Too few paired peaks (8) 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 00:02:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3159484/SRX3159484.10_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/SRX3159484/SRX3159484.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3159484/SRX3159484.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3159484/SRX3159484.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:02:55: 32000000 INFO @ Tue, 30 Jun 2020 00:03:03: 33000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:03:12: 34000000 INFO @ Tue, 30 Jun 2020 00:03:19: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 00:03:19: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 00:03:19: #1 total tags in treatment: 34863495 INFO @ Tue, 30 Jun 2020 00:03:19: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:03:19: #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 00:03:20: #1 tags after filtering in treatment: 34863495 INFO @ Tue, 30 Jun 2020 00:03:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:03:20: #1 finished! INFO @ Tue, 30 Jun 2020 00:03:20: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:03:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:03:22: #2 number of paired peaks: 8 WARNING @ Tue, 30 Jun 2020 00:03:22: Too few paired peaks (8) 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 00:03:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3159484/SRX3159484.20_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/SRX3159484/SRX3159484.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3159484/SRX3159484.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3159484/SRX3159484.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling