Job ID = 6527630 SRX = SRX1619260 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T12:46:22 prefetch.2.10.7: 1) Downloading 'SRR3211636'... 2020-06-29T12:46:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:52:49 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:52:49 prefetch.2.10.7: 1) 'SRR3211636' was downloaded successfully 2020-06-29T12:52:49 prefetch.2.10.7: 'SRR3211636' has 0 unresolved dependencies Read 34187023 spots for SRR3211636/SRR3211636.sra Written 34187023 spots for SRR3211636/SRR3211636.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: 00:00:01 Multiseed full-index search: 01:15:16 34187023 reads; of these: 34187023 (100.00%) were paired; of these: 8211250 (24.02%) aligned concordantly 0 times 20325164 (59.45%) aligned concordantly exactly 1 time 5650609 (16.53%) aligned concordantly >1 times ---- 8211250 pairs aligned concordantly 0 times; of these: 4688577 (57.10%) aligned discordantly 1 time ---- 3522673 pairs aligned 0 times concordantly or discordantly; of these: 7045346 mates make up the pairs; of these: 2812713 (39.92%) aligned 0 times 1984211 (28.16%) aligned exactly 1 time 2248422 (31.91%) aligned >1 times 95.89% overall alignment rate Time searching: 01:15:17 Overall time: 01:15:17 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 28 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] 5631468 / 30584011 = 0.1841 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 23:54:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1619260/SRX1619260.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1619260/SRX1619260.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1619260/SRX1619260.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1619260/SRX1619260.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 23:54:24: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:54:24: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:54:30: 1000000 INFO @ Mon, 29 Jun 2020 23:54:36: 2000000 INFO @ Mon, 29 Jun 2020 23:54:42: 3000000 INFO @ Mon, 29 Jun 2020 23:54:47: 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 23:54:53: 5000000 INFO @ Mon, 29 Jun 2020 23:54:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1619260/SRX1619260.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1619260/SRX1619260.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1619260/SRX1619260.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1619260/SRX1619260.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 23:54:54: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:54:54: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:54:59: 6000000 INFO @ Mon, 29 Jun 2020 23:55:01: 1000000 INFO @ Mon, 29 Jun 2020 23:55:06: 7000000 INFO @ Mon, 29 Jun 2020 23:55:07: 2000000 INFO @ Mon, 29 Jun 2020 23:55:12: 8000000 INFO @ Mon, 29 Jun 2020 23:55:14: 3000000 INFO @ Mon, 29 Jun 2020 23:55:19: 9000000 INFO @ Mon, 29 Jun 2020 23:55:20: 4000000 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 23:55:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1619260/SRX1619260.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1619260/SRX1619260.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1619260/SRX1619260.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1619260/SRX1619260.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 23:55:24: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:55:24: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:55:25: 10000000 INFO @ Mon, 29 Jun 2020 23:55:27: 5000000 INFO @ Mon, 29 Jun 2020 23:55:30: 1000000 INFO @ Mon, 29 Jun 2020 23:55:32: 11000000 INFO @ Mon, 29 Jun 2020 23:55:34: 6000000 INFO @ Mon, 29 Jun 2020 23:55:36: 2000000 INFO @ Mon, 29 Jun 2020 23:55:39: 12000000 INFO @ Mon, 29 Jun 2020 23:55:41: 7000000 INFO @ Mon, 29 Jun 2020 23:55:41: 3000000 INFO @ Mon, 29 Jun 2020 23:55:46: 13000000 INFO @ Mon, 29 Jun 2020 23:55:47: 4000000 INFO @ Mon, 29 Jun 2020 23:55:47: 8000000 INFO @ Mon, 29 Jun 2020 23:55:53: 5000000 INFO @ Mon, 29 Jun 2020 23:55:53: 14000000 INFO @ Mon, 29 Jun 2020 23:55:54: 9000000 INFO @ Mon, 29 Jun 2020 23:55:58: 6000000 INFO @ Mon, 29 Jun 2020 23:55:59: 15000000 INFO @ Mon, 29 Jun 2020 23:56:01: 10000000 INFO @ Mon, 29 Jun 2020 23:56:04: 7000000 INFO @ Mon, 29 Jun 2020 23:56:06: 16000000 INFO @ Mon, 29 Jun 2020 23:56:08: 11000000 INFO @ Mon, 29 Jun 2020 23:56:09: 8000000 INFO @ Mon, 29 Jun 2020 23:56:13: 17000000 INFO @ Mon, 29 Jun 2020 23:56:14: 12000000 INFO @ Mon, 29 Jun 2020 23:56:15: 9000000 INFO @ Mon, 29 Jun 2020 23:56:19: 18000000 INFO @ Mon, 29 Jun 2020 23:56:20: 10000000 INFO @ Mon, 29 Jun 2020 23:56:21: 13000000 INFO @ Mon, 29 Jun 2020 23:56:26: 11000000 INFO @ Mon, 29 Jun 2020 23:56:26: 19000000 INFO @ Mon, 29 Jun 2020 23:56:28: 14000000 INFO @ Mon, 29 Jun 2020 23:56:31: 12000000 INFO @ Mon, 29 Jun 2020 23:56:33: 20000000 INFO @ Mon, 29 Jun 2020 23:56:35: 15000000 INFO @ Mon, 29 Jun 2020 23:56:37: 13000000 INFO @ Mon, 29 Jun 2020 23:56:39: 21000000 INFO @ Mon, 29 Jun 2020 23:56:42: 16000000 INFO @ Mon, 29 Jun 2020 23:56:42: 14000000 INFO @ Mon, 29 Jun 2020 23:56:46: 22000000 INFO @ Mon, 29 Jun 2020 23:56:48: 15000000 INFO @ Mon, 29 Jun 2020 23:56:49: 17000000 INFO @ Mon, 29 Jun 2020 23:56:53: 23000000 INFO @ Mon, 29 Jun 2020 23:56:53: 16000000 INFO @ Mon, 29 Jun 2020 23:56:55: 18000000 INFO @ Mon, 29 Jun 2020 23:56:59: 17000000 INFO @ Mon, 29 Jun 2020 23:56:59: 24000000 INFO @ Mon, 29 Jun 2020 23:57:02: 19000000 INFO @ Mon, 29 Jun 2020 23:57:04: 18000000 INFO @ Mon, 29 Jun 2020 23:57:06: 25000000 INFO @ Mon, 29 Jun 2020 23:57:08: 20000000 INFO @ Mon, 29 Jun 2020 23:57:10: 19000000 INFO @ Mon, 29 Jun 2020 23:57:12: 26000000 INFO @ Mon, 29 Jun 2020 23:57:15: 20000000 INFO @ Mon, 29 Jun 2020 23:57:15: 21000000 INFO @ Mon, 29 Jun 2020 23:57:18: 27000000 INFO @ Mon, 29 Jun 2020 23:57:20: 21000000 INFO @ Mon, 29 Jun 2020 23:57:22: 22000000 INFO @ Mon, 29 Jun 2020 23:57:25: 28000000 INFO @ Mon, 29 Jun 2020 23:57:26: 22000000 INFO @ Mon, 29 Jun 2020 23:57:29: 23000000 INFO @ Mon, 29 Jun 2020 23:57:31: 23000000 INFO @ Mon, 29 Jun 2020 23:57:32: 29000000 INFO @ Mon, 29 Jun 2020 23:57:35: 24000000 INFO @ Mon, 29 Jun 2020 23:57:37: 24000000 INFO @ Mon, 29 Jun 2020 23:57:38: 30000000 INFO @ Mon, 29 Jun 2020 23:57:42: 25000000 INFO @ Mon, 29 Jun 2020 23:57:42: 25000000 INFO @ Mon, 29 Jun 2020 23:57:45: 31000000 INFO @ Mon, 29 Jun 2020 23:57:48: 26000000 INFO @ Mon, 29 Jun 2020 23:57:49: 26000000 INFO @ Mon, 29 Jun 2020 23:57:52: 32000000 INFO @ Mon, 29 Jun 2020 23:57:53: 27000000 INFO @ Mon, 29 Jun 2020 23:57:55: 27000000 INFO @ Mon, 29 Jun 2020 23:57:58: 33000000 INFO @ Mon, 29 Jun 2020 23:57:59: 28000000 INFO @ Mon, 29 Jun 2020 23:58:02: 28000000 INFO @ Mon, 29 Jun 2020 23:58:04: 29000000 INFO @ Mon, 29 Jun 2020 23:58:05: 34000000 INFO @ Mon, 29 Jun 2020 23:58:09: 29000000 INFO @ Mon, 29 Jun 2020 23:58:10: 30000000 INFO @ Mon, 29 Jun 2020 23:58:11: 35000000 INFO @ Mon, 29 Jun 2020 23:58:15: 31000000 INFO @ Mon, 29 Jun 2020 23:58:15: 30000000 INFO @ Mon, 29 Jun 2020 23:58:17: 36000000 INFO @ Mon, 29 Jun 2020 23:58:21: 32000000 INFO @ Mon, 29 Jun 2020 23:58:22: 31000000 INFO @ Mon, 29 Jun 2020 23:58:24: 37000000 INFO @ Mon, 29 Jun 2020 23:58:26: 33000000 INFO @ Mon, 29 Jun 2020 23:58:29: 32000000 INFO @ Mon, 29 Jun 2020 23:58:31: 38000000 INFO @ Mon, 29 Jun 2020 23:58:31: 34000000 INFO @ Mon, 29 Jun 2020 23:58:36: 33000000 INFO @ Mon, 29 Jun 2020 23:58:37: 35000000 INFO @ Mon, 29 Jun 2020 23:58:38: 39000000 INFO @ Mon, 29 Jun 2020 23:58:42: 34000000 INFO @ Mon, 29 Jun 2020 23:58:42: 36000000 INFO @ Mon, 29 Jun 2020 23:58:44: 40000000 INFO @ Mon, 29 Jun 2020 23:58:48: 37000000 INFO @ Mon, 29 Jun 2020 23:58:49: 35000000 INFO @ Mon, 29 Jun 2020 23:58:51: 41000000 INFO @ Mon, 29 Jun 2020 23:58:53: 38000000 INFO @ Mon, 29 Jun 2020 23:58:55: 36000000 INFO @ Mon, 29 Jun 2020 23:58:57: 42000000 INFO @ Mon, 29 Jun 2020 23:58:59: 39000000 INFO @ Mon, 29 Jun 2020 23:59:02: 37000000 INFO @ Mon, 29 Jun 2020 23:59:04: 43000000 INFO @ Mon, 29 Jun 2020 23:59:04: 40000000 INFO @ Mon, 29 Jun 2020 23:59:09: 38000000 INFO @ Mon, 29 Jun 2020 23:59:10: 41000000 INFO @ Mon, 29 Jun 2020 23:59:10: 44000000 INFO @ Mon, 29 Jun 2020 23:59:15: 42000000 INFO @ Mon, 29 Jun 2020 23:59:16: 39000000 INFO @ Mon, 29 Jun 2020 23:59:17: 45000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:59:21: 43000000 INFO @ Mon, 29 Jun 2020 23:59:22: 40000000 INFO @ Mon, 29 Jun 2020 23:59:24: 46000000 INFO @ Mon, 29 Jun 2020 23:59:26: 44000000 INFO @ Mon, 29 Jun 2020 23:59:29: 41000000 INFO @ Mon, 29 Jun 2020 23:59:30: 47000000 INFO @ Mon, 29 Jun 2020 23:59:32: 45000000 INFO @ Mon, 29 Jun 2020 23:59:36: 42000000 INFO @ Mon, 29 Jun 2020 23:59:37: 48000000 INFO @ Mon, 29 Jun 2020 23:59:37: 46000000 INFO @ Mon, 29 Jun 2020 23:59:42: 43000000 INFO @ Mon, 29 Jun 2020 23:59:43: 47000000 INFO @ Mon, 29 Jun 2020 23:59:44: 49000000 INFO @ Mon, 29 Jun 2020 23:59:48: 48000000 INFO @ Mon, 29 Jun 2020 23:59:48: 44000000 INFO @ Mon, 29 Jun 2020 23:59:51: 50000000 INFO @ Mon, 29 Jun 2020 23:59:54: 49000000 INFO @ Mon, 29 Jun 2020 23:59:55: 45000000 INFO @ Mon, 29 Jun 2020 23:59:57: 51000000 INFO @ Tue, 30 Jun 2020 00:00:00: 50000000 INFO @ Tue, 30 Jun 2020 00:00:02: 46000000 INFO @ Tue, 30 Jun 2020 00:00:04: 52000000 INFO @ Tue, 30 Jun 2020 00:00:05: 51000000 INFO @ Tue, 30 Jun 2020 00:00:08: 47000000 INFO @ Tue, 30 Jun 2020 00:00:11: 53000000 INFO @ Tue, 30 Jun 2020 00:00:11: 52000000 INFO @ Tue, 30 Jun 2020 00:00:15: 48000000 INFO @ Tue, 30 Jun 2020 00:00:16: 53000000 INFO @ Tue, 30 Jun 2020 00:00:17: 54000000 INFO @ Tue, 30 Jun 2020 00:00:19: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 00:00:19: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 00:00:19: #1 total tags in treatment: 20674170 INFO @ Tue, 30 Jun 2020 00:00:19: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:00:19: #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 00:00:20: #1 tags after filtering in treatment: 15379520 INFO @ Tue, 30 Jun 2020 00:00:20: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 30 Jun 2020 00:00:20: #1 finished! INFO @ Tue, 30 Jun 2020 00:00:20: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:00:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:00:21: #2 number of paired peaks: 52 WARNING @ Tue, 30 Jun 2020 00:00:21: Too few paired peaks (52) 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 00:00:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1619260/SRX1619260.05_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/SRX1619260/SRX1619260.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1619260/SRX1619260.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1619260/SRX1619260.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:00:22: 49000000 INFO @ Tue, 30 Jun 2020 00:00:22: 54000000 INFO @ Tue, 30 Jun 2020 00:00:24: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 00:00:24: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 00:00:24: #1 total tags in treatment: 20674170 INFO @ Tue, 30 Jun 2020 00:00:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:00:24: #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 00:00:24: #1 tags after filtering in treatment: 15379520 INFO @ Tue, 30 Jun 2020 00:00:24: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 30 Jun 2020 00:00:24: #1 finished! INFO @ Tue, 30 Jun 2020 00:00:24: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:00:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:00:25: #2 number of paired peaks: 52 WARNING @ Tue, 30 Jun 2020 00:00:25: Too few paired peaks (52) 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 00:00:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1619260/SRX1619260.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1619260/SRX1619260.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1619260/SRX1619260.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1619260/SRX1619260.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:00:28: 50000000 INFO @ Tue, 30 Jun 2020 00:00:34: 51000000 INFO @ Tue, 30 Jun 2020 00:00:40: 52000000 INFO @ Tue, 30 Jun 2020 00:00:45: 53000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:00:51: 54000000 INFO @ Tue, 30 Jun 2020 00:00:53: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 00:00:53: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 00:00:53: #1 total tags in treatment: 20674170 INFO @ Tue, 30 Jun 2020 00:00:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:00:53: #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 00:00:54: #1 tags after filtering in treatment: 15379520 INFO @ Tue, 30 Jun 2020 00:00:54: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 30 Jun 2020 00:00:54: #1 finished! INFO @ Tue, 30 Jun 2020 00:00:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:00:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:00:55: #2 number of paired peaks: 52 WARNING @ Tue, 30 Jun 2020 00:00:55: Too few paired peaks (52) 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 00:00:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1619260/SRX1619260.10_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/SRX1619260/SRX1619260.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1619260/SRX1619260.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1619260/SRX1619260.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling