Job ID = 6528001 SRX = SRX3723038 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:54:49 prefetch.2.10.7: 1) Downloading 'SRR6750396'... 2020-06-29T13:54:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:56:15 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:56:16 prefetch.2.10.7: 'SRR6750396' is valid 2020-06-29T13:56:16 prefetch.2.10.7: 1) 'SRR6750396' was downloaded successfully 2020-06-29T13:56:16 prefetch.2.10.7: 'SRR6750396' has 0 unresolved dependencies Read 12162861 spots for SRR6750396/SRR6750396.sra Written 12162861 spots for SRR6750396/SRR6750396.sra 2020-06-29T13:57:12 prefetch.2.10.7: 1) Downloading 'SRR6750397'... 2020-06-29T13:57:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:58:40 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:58:41 prefetch.2.10.7: 'SRR6750397' is valid 2020-06-29T13:58:41 prefetch.2.10.7: 1) 'SRR6750397' was downloaded successfully 2020-06-29T13:58:41 prefetch.2.10.7: 'SRR6750397' has 0 unresolved dependencies Read 12065374 spots for SRR6750397/SRR6750397.sra Written 12065374 spots for SRR6750397/SRR6750397.sra 2020-06-29T14:04:37 prefetch.2.10.7 int: connection failed while opening file within cryptographic module - cannot open remote file: https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR6750398/SRR6750398.1 2020-06-29T14:04:45 prefetch.2.10.7: 1) Downloading 'SRR6750398'... 2020-06-29T14:04:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:07:13 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:07:14 prefetch.2.10.7: 'SRR6750398' is valid 2020-06-29T14:07:14 prefetch.2.10.7: 1) 'SRR6750398' was downloaded successfully 2020-06-29T14:07:14 prefetch.2.10.7: 'SRR6750398' has 0 unresolved dependencies Read 12710394 spots for SRR6750398/SRR6750398.sra Written 12710394 spots for SRR6750398/SRR6750398.sra 2020-06-29T14:08:14 prefetch.2.10.7: 1) Downloading 'SRR6750399'... 2020-06-29T14:08:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:11:20 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:11:20 prefetch.2.10.7: 'SRR6750399' is valid 2020-06-29T14:11:20 prefetch.2.10.7: 1) 'SRR6750399' was downloaded successfully 2020-06-29T14:11:20 prefetch.2.10.7: 'SRR6750399' has 0 unresolved dependencies Read 12580450 spots for SRR6750399/SRR6750399.sra Written 12580450 spots for SRR6750399/SRR6750399.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: 00:15:18 49519079 reads; of these: 49519079 (100.00%) were unpaired; of these: 19762489 (39.91%) aligned 0 times 21550306 (43.52%) aligned exactly 1 time 8206284 (16.57%) aligned >1 times 60.09% overall alignment rate Time searching: 00:15:18 Overall time: 00:15:18 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_rmdupse_core] 6344484 / 29756590 = 0.2132 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 23:55:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3723038/SRX3723038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3723038/SRX3723038.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3723038/SRX3723038.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3723038/SRX3723038.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 23:55:31: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:55:31: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:55:38: 1000000 INFO @ Mon, 29 Jun 2020 23:55:45: 2000000 INFO @ Mon, 29 Jun 2020 23:55:51: 3000000 INFO @ Mon, 29 Jun 2020 23:55:58: 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 23:56:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3723038/SRX3723038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3723038/SRX3723038.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3723038/SRX3723038.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3723038/SRX3723038.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 23:56:01: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:56:01: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:56:05: 5000000 INFO @ Mon, 29 Jun 2020 23:56:09: 1000000 INFO @ Mon, 29 Jun 2020 23:56:13: 6000000 INFO @ Mon, 29 Jun 2020 23:56:16: 2000000 INFO @ Mon, 29 Jun 2020 23:56:20: 7000000 INFO @ Mon, 29 Jun 2020 23:56:24: 3000000 INFO @ Mon, 29 Jun 2020 23:56:28: 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 23:56:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3723038/SRX3723038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3723038/SRX3723038.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3723038/SRX3723038.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3723038/SRX3723038.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 23:56:31: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:56:31: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:56:32: 4000000 INFO @ Mon, 29 Jun 2020 23:56:36: 9000000 INFO @ Mon, 29 Jun 2020 23:56:39: 1000000 INFO @ Mon, 29 Jun 2020 23:56:39: 5000000 INFO @ Mon, 29 Jun 2020 23:56:43: 10000000 INFO @ Mon, 29 Jun 2020 23:56:47: 2000000 INFO @ Mon, 29 Jun 2020 23:56:47: 6000000 INFO @ Mon, 29 Jun 2020 23:56:51: 11000000 INFO @ Mon, 29 Jun 2020 23:56:55: 3000000 INFO @ Mon, 29 Jun 2020 23:56:55: 7000000 INFO @ Mon, 29 Jun 2020 23:56:58: 12000000 INFO @ Mon, 29 Jun 2020 23:57:03: 4000000 INFO @ Mon, 29 Jun 2020 23:57:03: 8000000 INFO @ Mon, 29 Jun 2020 23:57:06: 13000000 INFO @ Mon, 29 Jun 2020 23:57:11: 5000000 INFO @ Mon, 29 Jun 2020 23:57:11: 9000000 INFO @ Mon, 29 Jun 2020 23:57:14: 14000000 INFO @ Mon, 29 Jun 2020 23:57:19: 6000000 INFO @ Mon, 29 Jun 2020 23:57:19: 10000000 INFO @ Mon, 29 Jun 2020 23:57:22: 15000000 INFO @ Mon, 29 Jun 2020 23:57:27: 11000000 INFO @ Mon, 29 Jun 2020 23:57:27: 7000000 INFO @ Mon, 29 Jun 2020 23:57:29: 16000000 INFO @ Mon, 29 Jun 2020 23:57:35: 12000000 INFO @ Mon, 29 Jun 2020 23:57:35: 8000000 INFO @ Mon, 29 Jun 2020 23:57:37: 17000000 INFO @ Mon, 29 Jun 2020 23:57:42: 13000000 INFO @ Mon, 29 Jun 2020 23:57:43: 9000000 INFO @ Mon, 29 Jun 2020 23:57:44: 18000000 INFO @ Mon, 29 Jun 2020 23:57:50: 14000000 INFO @ Mon, 29 Jun 2020 23:57:50: 10000000 INFO @ Mon, 29 Jun 2020 23:57:52: 19000000 INFO @ Mon, 29 Jun 2020 23:57:58: 15000000 INFO @ Mon, 29 Jun 2020 23:57:58: 11000000 INFO @ Mon, 29 Jun 2020 23:58:00: 20000000 INFO @ Mon, 29 Jun 2020 23:58:05: 16000000 INFO @ Mon, 29 Jun 2020 23:58:06: 12000000 INFO @ Mon, 29 Jun 2020 23:58:07: 21000000 INFO @ Mon, 29 Jun 2020 23:58:13: 17000000 INFO @ Mon, 29 Jun 2020 23:58:13: 13000000 INFO @ Mon, 29 Jun 2020 23:58:15: 22000000 INFO @ Mon, 29 Jun 2020 23:58:21: 18000000 INFO @ Mon, 29 Jun 2020 23:58:21: 14000000 INFO @ Mon, 29 Jun 2020 23:58:23: 23000000 INFO @ Mon, 29 Jun 2020 23:58:26: #1 tag size is determined as 76 bps INFO @ Mon, 29 Jun 2020 23:58:26: #1 tag size = 76 INFO @ Mon, 29 Jun 2020 23:58:26: #1 total tags in treatment: 23412106 INFO @ Mon, 29 Jun 2020 23:58:26: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:58:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:58:26: #1 tags after filtering in treatment: 23412106 INFO @ Mon, 29 Jun 2020 23:58:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:58:26: #1 finished! INFO @ Mon, 29 Jun 2020 23:58:26: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:58:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:58:28: #2 number of paired peaks: 17 WARNING @ Mon, 29 Jun 2020 23:58:28: Too few paired peaks (17) 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 @ Mon, 29 Jun 2020 23:58:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3723038/SRX3723038.05_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/SRX3723038/SRX3723038.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3723038/SRX3723038.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3723038/SRX3723038.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:58:28: 19000000 INFO @ Mon, 29 Jun 2020 23:58:28: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:58:35: 20000000 INFO @ Mon, 29 Jun 2020 23:58:36: 16000000 INFO @ Mon, 29 Jun 2020 23:58:43: 21000000 INFO @ Mon, 29 Jun 2020 23:58:43: 17000000 INFO @ Mon, 29 Jun 2020 23:58:50: 22000000 INFO @ Mon, 29 Jun 2020 23:58:50: 18000000 INFO @ Mon, 29 Jun 2020 23:58:57: 23000000 INFO @ Mon, 29 Jun 2020 23:58:57: 19000000 INFO @ Mon, 29 Jun 2020 23:59:00: #1 tag size is determined as 76 bps INFO @ Mon, 29 Jun 2020 23:59:00: #1 tag size = 76 INFO @ Mon, 29 Jun 2020 23:59:00: #1 total tags in treatment: 23412106 INFO @ Mon, 29 Jun 2020 23:59:00: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:59:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:59:00: #1 tags after filtering in treatment: 23412106 INFO @ Mon, 29 Jun 2020 23:59:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:59:00: #1 finished! INFO @ Mon, 29 Jun 2020 23:59:00: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:59:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:59:02: #2 number of paired peaks: 17 WARNING @ Mon, 29 Jun 2020 23:59:02: Too few paired peaks (17) 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 @ Mon, 29 Jun 2020 23:59:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3723038/SRX3723038.10_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/SRX3723038/SRX3723038.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3723038/SRX3723038.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3723038/SRX3723038.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:59:04: 20000000 INFO @ Mon, 29 Jun 2020 23:59:11: 21000000 INFO @ Mon, 29 Jun 2020 23:59:18: 22000000 INFO @ Mon, 29 Jun 2020 23:59:24: 23000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:59:27: #1 tag size is determined as 76 bps INFO @ Mon, 29 Jun 2020 23:59:27: #1 tag size = 76 INFO @ Mon, 29 Jun 2020 23:59:27: #1 total tags in treatment: 23412106 INFO @ Mon, 29 Jun 2020 23:59:27: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:59:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:59:28: #1 tags after filtering in treatment: 23412106 INFO @ Mon, 29 Jun 2020 23:59:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:59:28: #1 finished! INFO @ Mon, 29 Jun 2020 23:59:28: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:59:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:59:29: #2 number of paired peaks: 17 WARNING @ Mon, 29 Jun 2020 23:59:29: Too few paired peaks (17) 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 @ Mon, 29 Jun 2020 23:59:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3723038/SRX3723038.20_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/SRX3723038/SRX3723038.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3723038/SRX3723038.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3723038/SRX3723038.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling