Job ID = 6527926 SRX = SRX3293409 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T13:54:15 prefetch.2.10.7: 1) Downloading 'SRR6183236'... 2020-06-29T13:54:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:56:46 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:56:46 prefetch.2.10.7: 1) 'SRR6183236' was downloaded successfully 2020-06-29T13:56:46 prefetch.2.10.7: 'SRR6183236' has 0 unresolved dependencies Read 25611183 spots for SRR6183236/SRR6183236.sra Written 25611183 spots for SRR6183236/SRR6183236.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: 00:43:28 25611183 reads; of these: 25611183 (100.00%) were paired; of these: 2636420 (10.29%) aligned concordantly 0 times 14064401 (54.92%) aligned concordantly exactly 1 time 8910362 (34.79%) aligned concordantly >1 times ---- 2636420 pairs aligned concordantly 0 times; of these: 336031 (12.75%) aligned discordantly 1 time ---- 2300389 pairs aligned 0 times concordantly or discordantly; of these: 4600778 mates make up the pairs; of these: 3195089 (69.45%) aligned 0 times 765255 (16.63%) aligned exactly 1 time 640434 (13.92%) aligned >1 times 93.76% overall alignment rate Time searching: 00:43:28 Overall time: 00:43:28 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] 2865223 / 23231641 = 0.1233 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 23:58:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3293409/SRX3293409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3293409/SRX3293409.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3293409/SRX3293409.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3293409/SRX3293409.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 23:58:30: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:58:30: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:58:35: 1000000 INFO @ Mon, 29 Jun 2020 23:58:39: 2000000 INFO @ Mon, 29 Jun 2020 23:58:44: 3000000 INFO @ Mon, 29 Jun 2020 23:58:49: 4000000 INFO @ Mon, 29 Jun 2020 23:58:53: 5000000 INFO @ Mon, 29 Jun 2020 23:58:58: 6000000 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 23:59:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3293409/SRX3293409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3293409/SRX3293409.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3293409/SRX3293409.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3293409/SRX3293409.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 23:59:00: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:59:00: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:59:03: 7000000 INFO @ Mon, 29 Jun 2020 23:59:05: 1000000 INFO @ Mon, 29 Jun 2020 23:59:07: 8000000 INFO @ Mon, 29 Jun 2020 23:59:10: 2000000 INFO @ Mon, 29 Jun 2020 23:59:12: 9000000 INFO @ Mon, 29 Jun 2020 23:59:15: 3000000 INFO @ Mon, 29 Jun 2020 23:59:17: 10000000 INFO @ Mon, 29 Jun 2020 23:59:20: 4000000 INFO @ Mon, 29 Jun 2020 23:59:22: 11000000 INFO @ Mon, 29 Jun 2020 23:59:25: 5000000 INFO @ Mon, 29 Jun 2020 23:59:27: 12000000 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 23:59:29: 6000000 INFO @ Mon, 29 Jun 2020 23:59:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3293409/SRX3293409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3293409/SRX3293409.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3293409/SRX3293409.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3293409/SRX3293409.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 23:59:30: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:59:30: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:59:32: 13000000 INFO @ Mon, 29 Jun 2020 23:59:34: 7000000 INFO @ Mon, 29 Jun 2020 23:59:35: 1000000 INFO @ Mon, 29 Jun 2020 23:59:37: 14000000 INFO @ Mon, 29 Jun 2020 23:59:38: 8000000 INFO @ Mon, 29 Jun 2020 23:59:40: 2000000 INFO @ Mon, 29 Jun 2020 23:59:42: 15000000 INFO @ Mon, 29 Jun 2020 23:59:42: 9000000 INFO @ Mon, 29 Jun 2020 23:59:45: 3000000 INFO @ Mon, 29 Jun 2020 23:59:47: 16000000 INFO @ Mon, 29 Jun 2020 23:59:47: 10000000 INFO @ Mon, 29 Jun 2020 23:59:50: 4000000 INFO @ Mon, 29 Jun 2020 23:59:51: 11000000 INFO @ Mon, 29 Jun 2020 23:59:51: 17000000 INFO @ Mon, 29 Jun 2020 23:59:55: 5000000 INFO @ Mon, 29 Jun 2020 23:59:56: 12000000 INFO @ Mon, 29 Jun 2020 23:59:56: 18000000 INFO @ Tue, 30 Jun 2020 00:00:00: 13000000 INFO @ Tue, 30 Jun 2020 00:00:00: 6000000 INFO @ Tue, 30 Jun 2020 00:00:01: 19000000 INFO @ Tue, 30 Jun 2020 00:00:05: 14000000 INFO @ Tue, 30 Jun 2020 00:00:05: 7000000 INFO @ Tue, 30 Jun 2020 00:00:06: 20000000 INFO @ Tue, 30 Jun 2020 00:00:10: 15000000 INFO @ Tue, 30 Jun 2020 00:00:11: 8000000 INFO @ Tue, 30 Jun 2020 00:00:11: 21000000 INFO @ Tue, 30 Jun 2020 00:00:14: 16000000 INFO @ Tue, 30 Jun 2020 00:00:16: 9000000 INFO @ Tue, 30 Jun 2020 00:00:16: 22000000 INFO @ Tue, 30 Jun 2020 00:00:19: 17000000 INFO @ Tue, 30 Jun 2020 00:00:21: 10000000 INFO @ Tue, 30 Jun 2020 00:00:21: 23000000 INFO @ Tue, 30 Jun 2020 00:00:24: 18000000 INFO @ Tue, 30 Jun 2020 00:00:25: 11000000 INFO @ Tue, 30 Jun 2020 00:00:26: 24000000 INFO @ Tue, 30 Jun 2020 00:00:28: 19000000 INFO @ Tue, 30 Jun 2020 00:00:30: 12000000 INFO @ Tue, 30 Jun 2020 00:00:31: 25000000 INFO @ Tue, 30 Jun 2020 00:00:33: 20000000 INFO @ Tue, 30 Jun 2020 00:00:35: 13000000 INFO @ Tue, 30 Jun 2020 00:00:36: 26000000 INFO @ Tue, 30 Jun 2020 00:00:37: 21000000 INFO @ Tue, 30 Jun 2020 00:00:40: 14000000 INFO @ Tue, 30 Jun 2020 00:00:41: 27000000 INFO @ Tue, 30 Jun 2020 00:00:42: 22000000 INFO @ Tue, 30 Jun 2020 00:00:45: 15000000 INFO @ Tue, 30 Jun 2020 00:00:45: 28000000 INFO @ Tue, 30 Jun 2020 00:00:47: 23000000 INFO @ Tue, 30 Jun 2020 00:00:50: 29000000 INFO @ Tue, 30 Jun 2020 00:00:50: 16000000 INFO @ Tue, 30 Jun 2020 00:00:51: 24000000 INFO @ Tue, 30 Jun 2020 00:00:55: 30000000 INFO @ Tue, 30 Jun 2020 00:00:55: 17000000 INFO @ Tue, 30 Jun 2020 00:00:56: 25000000 INFO @ Tue, 30 Jun 2020 00:01:00: 18000000 INFO @ Tue, 30 Jun 2020 00:01:01: 31000000 INFO @ Tue, 30 Jun 2020 00:01:01: 26000000 INFO @ Tue, 30 Jun 2020 00:01:05: 27000000 INFO @ Tue, 30 Jun 2020 00:01:06: 19000000 INFO @ Tue, 30 Jun 2020 00:01:06: 32000000 INFO @ Tue, 30 Jun 2020 00:01:10: 28000000 INFO @ Tue, 30 Jun 2020 00:01:10: 20000000 INFO @ Tue, 30 Jun 2020 00:01:10: 33000000 INFO @ Tue, 30 Jun 2020 00:01:15: 29000000 INFO @ Tue, 30 Jun 2020 00:01:15: 34000000 INFO @ Tue, 30 Jun 2020 00:01:15: 21000000 INFO @ Tue, 30 Jun 2020 00:01:19: 30000000 INFO @ Tue, 30 Jun 2020 00:01:20: 35000000 INFO @ Tue, 30 Jun 2020 00:01:20: 22000000 INFO @ Tue, 30 Jun 2020 00:01:23: 31000000 INFO @ Tue, 30 Jun 2020 00:01:25: 36000000 INFO @ Tue, 30 Jun 2020 00:01:25: 23000000 INFO @ Tue, 30 Jun 2020 00:01:28: 32000000 INFO @ Tue, 30 Jun 2020 00:01:29: 37000000 INFO @ Tue, 30 Jun 2020 00:01:30: 24000000 INFO @ Tue, 30 Jun 2020 00:01:32: 33000000 INFO @ Tue, 30 Jun 2020 00:01:34: 38000000 INFO @ Tue, 30 Jun 2020 00:01:35: 25000000 INFO @ Tue, 30 Jun 2020 00:01:36: 34000000 INFO @ Tue, 30 Jun 2020 00:01:39: 39000000 INFO @ Tue, 30 Jun 2020 00:01:40: 26000000 INFO @ Tue, 30 Jun 2020 00:01:40: 35000000 INFO @ Tue, 30 Jun 2020 00:01:44: 40000000 INFO @ Tue, 30 Jun 2020 00:01:45: 36000000 INFO @ Tue, 30 Jun 2020 00:01:45: 27000000 INFO @ Tue, 30 Jun 2020 00:01:49: 37000000 INFO @ Tue, 30 Jun 2020 00:01:49: 41000000 INFO @ Tue, 30 Jun 2020 00:01:50: 28000000 INFO @ Tue, 30 Jun 2020 00:01:53: 38000000 INFO @ Tue, 30 Jun 2020 00:01:54: 42000000 INFO @ Tue, 30 Jun 2020 00:01:55: 29000000 INFO @ Tue, 30 Jun 2020 00:01:55: #1 tag size is determined as 25 bps INFO @ Tue, 30 Jun 2020 00:01:55: #1 tag size = 25 INFO @ Tue, 30 Jun 2020 00:01:55: #1 total tags in treatment: 20110309 INFO @ Tue, 30 Jun 2020 00:01:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:01:55: #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 00:01:56: #1 tags after filtering in treatment: 16378284 INFO @ Tue, 30 Jun 2020 00:01:56: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 30 Jun 2020 00:01:56: #1 finished! INFO @ Tue, 30 Jun 2020 00:01:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:01:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:01:57: #2 number of paired peaks: 31 WARNING @ Tue, 30 Jun 2020 00:01:57: Too few paired peaks (31) 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 00:01:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3293409/SRX3293409.05_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/SRX3293409/SRX3293409.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3293409/SRX3293409.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3293409/SRX3293409.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:01:57: 39000000 INFO @ Tue, 30 Jun 2020 00:02:00: 30000000 INFO @ Tue, 30 Jun 2020 00:02:02: 40000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:02:04: 31000000 INFO @ Tue, 30 Jun 2020 00:02:06: 41000000 INFO @ Tue, 30 Jun 2020 00:02:09: 32000000 INFO @ Tue, 30 Jun 2020 00:02:10: 42000000 INFO @ Tue, 30 Jun 2020 00:02:12: #1 tag size is determined as 25 bps INFO @ Tue, 30 Jun 2020 00:02:12: #1 tag size = 25 INFO @ Tue, 30 Jun 2020 00:02:12: #1 total tags in treatment: 20110309 INFO @ Tue, 30 Jun 2020 00:02:12: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:02:12: #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 00:02:12: #1 tags after filtering in treatment: 16378284 INFO @ Tue, 30 Jun 2020 00:02:12: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 30 Jun 2020 00:02:12: #1 finished! INFO @ Tue, 30 Jun 2020 00:02:12: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:02:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:02:13: #2 number of paired peaks: 31 WARNING @ Tue, 30 Jun 2020 00:02:13: Too few paired peaks (31) 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 00:02:13: Process for pairing-model is terminated! INFO @ Tue, 30 Jun 2020 00:02:14: 33000000 cut: /home/okishinya/chipatlas/results/dm3/SRX3293409/SRX3293409.10_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/SRX3293409/SRX3293409.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3293409/SRX3293409.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3293409/SRX3293409.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:02:19: 34000000 INFO @ Tue, 30 Jun 2020 00:02:23: 35000000 INFO @ Tue, 30 Jun 2020 00:02:28: 36000000 INFO @ Tue, 30 Jun 2020 00:02:32: 37000000 INFO @ Tue, 30 Jun 2020 00:02:37: 38000000 INFO @ Tue, 30 Jun 2020 00:02:42: 39000000 INFO @ Tue, 30 Jun 2020 00:02:47: 40000000 INFO @ Tue, 30 Jun 2020 00:02:51: 41000000 INFO @ Tue, 30 Jun 2020 00:02:56: 42000000 INFO @ Tue, 30 Jun 2020 00:02:58: #1 tag size is determined as 25 bps INFO @ Tue, 30 Jun 2020 00:02:58: #1 tag size = 25 INFO @ Tue, 30 Jun 2020 00:02:58: #1 total tags in treatment: 20110309 INFO @ Tue, 30 Jun 2020 00:02:58: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:02:58: #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 00:02:58: #1 tags after filtering in treatment: 16378284 INFO @ Tue, 30 Jun 2020 00:02:58: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 30 Jun 2020 00:02:58: #1 finished! INFO @ Tue, 30 Jun 2020 00:02:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:02:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:02:59: #2 number of paired peaks: 31 WARNING @ Tue, 30 Jun 2020 00:02:59: Too few paired peaks (31) 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 00:02:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3293409/SRX3293409.20_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/SRX3293409/SRX3293409.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3293409/SRX3293409.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3293409/SRX3293409.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。