Job ID = 6527631 SRX = SRX1704844 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T13:08:09 prefetch.2.10.7: 1) Downloading 'SRR3383178'... 2020-06-29T13:08:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:14:36 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:14:36 prefetch.2.10.7: 1) 'SRR3383178' was downloaded successfully 2020-06-29T13:14:36 prefetch.2.10.7: 'SRR3383178' has 0 unresolved dependencies Read 29856567 spots for SRR3383178/SRR3383178.sra Written 29856567 spots for SRR3383178/SRR3383178.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: 01:09:09 29856567 reads; of these: 29856567 (100.00%) were paired; of these: 2711441 (9.08%) aligned concordantly 0 times 18805656 (62.99%) aligned concordantly exactly 1 time 8339470 (27.93%) aligned concordantly >1 times ---- 2711441 pairs aligned concordantly 0 times; of these: 928224 (34.23%) aligned discordantly 1 time ---- 1783217 pairs aligned 0 times concordantly or discordantly; of these: 3566434 mates make up the pairs; of these: 1551482 (43.50%) aligned 0 times 959069 (26.89%) aligned exactly 1 time 1055883 (29.61%) aligned >1 times 97.40% overall alignment rate Time searching: 01:09:09 Overall time: 01:09:09 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 24 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] 3531805 / 27866319 = 0.1267 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 23:56:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1704844/SRX1704844.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1704844/SRX1704844.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1704844/SRX1704844.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1704844/SRX1704844.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 23:56:48: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:56:48: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:56:53: 1000000 INFO @ Mon, 29 Jun 2020 23:56:59: 2000000 INFO @ Mon, 29 Jun 2020 23:57:04: 3000000 INFO @ Mon, 29 Jun 2020 23:57:09: 4000000 INFO @ Mon, 29 Jun 2020 23:57:15: 5000000 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 23:57:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1704844/SRX1704844.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1704844/SRX1704844.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1704844/SRX1704844.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1704844/SRX1704844.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 23:57:18: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:57:18: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:57:21: 6000000 INFO @ Mon, 29 Jun 2020 23:57:25: 1000000 INFO @ Mon, 29 Jun 2020 23:57:27: 7000000 INFO @ Mon, 29 Jun 2020 23:57:31: 2000000 INFO @ Mon, 29 Jun 2020 23:57:34: 8000000 INFO @ Mon, 29 Jun 2020 23:57:37: 3000000 INFO @ Mon, 29 Jun 2020 23:57:40: 9000000 INFO @ Mon, 29 Jun 2020 23:57:44: 4000000 INFO @ Mon, 29 Jun 2020 23:57:46: 10000000 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 23:57:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1704844/SRX1704844.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1704844/SRX1704844.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1704844/SRX1704844.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1704844/SRX1704844.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 23:57:48: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:57:48: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:57:50: 5000000 INFO @ Mon, 29 Jun 2020 23:57:52: 11000000 INFO @ Mon, 29 Jun 2020 23:57:54: 1000000 INFO @ Mon, 29 Jun 2020 23:57:56: 6000000 INFO @ Mon, 29 Jun 2020 23:57:59: 12000000 INFO @ Mon, 29 Jun 2020 23:58:01: 2000000 INFO @ Mon, 29 Jun 2020 23:58:03: 7000000 INFO @ Mon, 29 Jun 2020 23:58:05: 13000000 INFO @ Mon, 29 Jun 2020 23:58:07: 3000000 INFO @ Mon, 29 Jun 2020 23:58:10: 8000000 INFO @ Mon, 29 Jun 2020 23:58:12: 14000000 INFO @ Mon, 29 Jun 2020 23:58:13: 4000000 INFO @ Mon, 29 Jun 2020 23:58:16: 9000000 INFO @ Mon, 29 Jun 2020 23:58:18: 15000000 INFO @ Mon, 29 Jun 2020 23:58:20: 5000000 INFO @ Mon, 29 Jun 2020 23:58:23: 10000000 INFO @ Mon, 29 Jun 2020 23:58:25: 16000000 INFO @ Mon, 29 Jun 2020 23:58:26: 6000000 INFO @ Mon, 29 Jun 2020 23:58:29: 11000000 INFO @ Mon, 29 Jun 2020 23:58:31: 17000000 INFO @ Mon, 29 Jun 2020 23:58:32: 7000000 INFO @ Mon, 29 Jun 2020 23:58:36: 12000000 INFO @ Mon, 29 Jun 2020 23:58:38: 18000000 INFO @ Mon, 29 Jun 2020 23:58:38: 8000000 INFO @ Mon, 29 Jun 2020 23:58:42: 13000000 INFO @ Mon, 29 Jun 2020 23:58:44: 19000000 INFO @ Mon, 29 Jun 2020 23:58:45: 9000000 INFO @ Mon, 29 Jun 2020 23:58:48: 14000000 INFO @ Mon, 29 Jun 2020 23:58:51: 10000000 INFO @ Mon, 29 Jun 2020 23:58:51: 20000000 INFO @ Mon, 29 Jun 2020 23:58:55: 15000000 INFO @ Mon, 29 Jun 2020 23:58:57: 11000000 INFO @ Mon, 29 Jun 2020 23:58:57: 21000000 INFO @ Mon, 29 Jun 2020 23:59:01: 16000000 INFO @ Mon, 29 Jun 2020 23:59:03: 12000000 INFO @ Mon, 29 Jun 2020 23:59:04: 22000000 INFO @ Mon, 29 Jun 2020 23:59:08: 17000000 INFO @ Mon, 29 Jun 2020 23:59:09: 13000000 INFO @ Mon, 29 Jun 2020 23:59:10: 23000000 INFO @ Mon, 29 Jun 2020 23:59:14: 18000000 INFO @ Mon, 29 Jun 2020 23:59:15: 14000000 INFO @ Mon, 29 Jun 2020 23:59:16: 24000000 INFO @ Mon, 29 Jun 2020 23:59:20: 19000000 INFO @ Mon, 29 Jun 2020 23:59:21: 15000000 INFO @ Mon, 29 Jun 2020 23:59:23: 25000000 INFO @ Mon, 29 Jun 2020 23:59:27: 20000000 INFO @ Mon, 29 Jun 2020 23:59:28: 16000000 INFO @ Mon, 29 Jun 2020 23:59:29: 26000000 INFO @ Mon, 29 Jun 2020 23:59:34: 21000000 INFO @ Mon, 29 Jun 2020 23:59:35: 17000000 INFO @ Mon, 29 Jun 2020 23:59:36: 27000000 INFO @ Mon, 29 Jun 2020 23:59:41: 22000000 INFO @ Mon, 29 Jun 2020 23:59:42: 18000000 INFO @ Mon, 29 Jun 2020 23:59:43: 28000000 INFO @ Mon, 29 Jun 2020 23:59:49: 23000000 INFO @ Mon, 29 Jun 2020 23:59:50: 19000000 INFO @ Mon, 29 Jun 2020 23:59:50: 29000000 INFO @ Mon, 29 Jun 2020 23:59:56: 24000000 INFO @ Mon, 29 Jun 2020 23:59:57: 20000000 INFO @ Mon, 29 Jun 2020 23:59:57: 30000000 INFO @ Tue, 30 Jun 2020 00:00:03: 25000000 INFO @ Tue, 30 Jun 2020 00:00:04: 21000000 INFO @ Tue, 30 Jun 2020 00:00:04: 31000000 INFO @ Tue, 30 Jun 2020 00:00:10: 26000000 INFO @ Tue, 30 Jun 2020 00:00:11: 32000000 INFO @ Tue, 30 Jun 2020 00:00:12: 22000000 INFO @ Tue, 30 Jun 2020 00:00:17: 27000000 INFO @ Tue, 30 Jun 2020 00:00:18: 33000000 INFO @ Tue, 30 Jun 2020 00:00:19: 23000000 INFO @ Tue, 30 Jun 2020 00:00:24: 28000000 INFO @ Tue, 30 Jun 2020 00:00:26: 34000000 INFO @ Tue, 30 Jun 2020 00:00:26: 24000000 INFO @ Tue, 30 Jun 2020 00:00:32: 29000000 INFO @ Tue, 30 Jun 2020 00:00:33: 35000000 INFO @ Tue, 30 Jun 2020 00:00:33: 25000000 INFO @ Tue, 30 Jun 2020 00:00:39: 30000000 INFO @ Tue, 30 Jun 2020 00:00:40: 36000000 INFO @ Tue, 30 Jun 2020 00:00:41: 26000000 INFO @ Tue, 30 Jun 2020 00:00:46: 31000000 INFO @ Tue, 30 Jun 2020 00:00:47: 37000000 INFO @ Tue, 30 Jun 2020 00:00:48: 27000000 INFO @ Tue, 30 Jun 2020 00:00:53: 32000000 INFO @ Tue, 30 Jun 2020 00:00:55: 38000000 INFO @ Tue, 30 Jun 2020 00:00:56: 28000000 INFO @ Tue, 30 Jun 2020 00:01:00: 33000000 INFO @ Tue, 30 Jun 2020 00:01:02: 39000000 INFO @ Tue, 30 Jun 2020 00:01:03: 29000000 INFO @ Tue, 30 Jun 2020 00:01:07: 34000000 INFO @ Tue, 30 Jun 2020 00:01:09: 40000000 INFO @ Tue, 30 Jun 2020 00:01:10: 30000000 INFO @ Tue, 30 Jun 2020 00:01:14: 35000000 INFO @ Tue, 30 Jun 2020 00:01:16: 41000000 INFO @ Tue, 30 Jun 2020 00:01:18: 31000000 INFO @ Tue, 30 Jun 2020 00:01:21: 36000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:01:23: 42000000 INFO @ Tue, 30 Jun 2020 00:01:25: 32000000 INFO @ Tue, 30 Jun 2020 00:01:28: 37000000 INFO @ Tue, 30 Jun 2020 00:01:30: 43000000 INFO @ Tue, 30 Jun 2020 00:01:33: 33000000 INFO @ Tue, 30 Jun 2020 00:01:35: 38000000 INFO @ Tue, 30 Jun 2020 00:01:38: 44000000 INFO @ Tue, 30 Jun 2020 00:01:40: 34000000 INFO @ Tue, 30 Jun 2020 00:01:43: 39000000 INFO @ Tue, 30 Jun 2020 00:01:45: 45000000 INFO @ Tue, 30 Jun 2020 00:01:47: 35000000 INFO @ Tue, 30 Jun 2020 00:01:50: 40000000 INFO @ Tue, 30 Jun 2020 00:01:52: 46000000 INFO @ Tue, 30 Jun 2020 00:01:55: 36000000 INFO @ Tue, 30 Jun 2020 00:01:57: 41000000 INFO @ Tue, 30 Jun 2020 00:01:59: 47000000 INFO @ Tue, 30 Jun 2020 00:02:02: 37000000 INFO @ Tue, 30 Jun 2020 00:02:04: 42000000 INFO @ Tue, 30 Jun 2020 00:02:06: 48000000 INFO @ Tue, 30 Jun 2020 00:02:09: 38000000 INFO @ Tue, 30 Jun 2020 00:02:11: 43000000 INFO @ Tue, 30 Jun 2020 00:02:13: 49000000 INFO @ Tue, 30 Jun 2020 00:02:17: 39000000 INFO @ Tue, 30 Jun 2020 00:02:18: 44000000 INFO @ Tue, 30 Jun 2020 00:02:20: 50000000 INFO @ Tue, 30 Jun 2020 00:02:24: 40000000 INFO @ Tue, 30 Jun 2020 00:02:25: 45000000 INFO @ Tue, 30 Jun 2020 00:02:26: 51000000 INFO @ Tue, 30 Jun 2020 00:02:27: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 00:02:27: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 00:02:27: #1 total tags in treatment: 23628856 INFO @ Tue, 30 Jun 2020 00:02:27: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:02:27: #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 00:02:27: #1 tags after filtering in treatment: 17110447 INFO @ Tue, 30 Jun 2020 00:02:27: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 30 Jun 2020 00:02:27: #1 finished! INFO @ Tue, 30 Jun 2020 00:02:27: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:02:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:02:29: #2 number of paired peaks: 41 WARNING @ Tue, 30 Jun 2020 00:02:29: Too few paired peaks (41) 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 00:02:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1704844/SRX1704844.05_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/SRX1704844/SRX1704844.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1704844/SRX1704844.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1704844/SRX1704844.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:02:31: 46000000 INFO @ Tue, 30 Jun 2020 00:02:31: 41000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:02:37: 47000000 INFO @ Tue, 30 Jun 2020 00:02:39: 42000000 INFO @ Tue, 30 Jun 2020 00:02:44: 48000000 INFO @ Tue, 30 Jun 2020 00:02:46: 43000000 INFO @ Tue, 30 Jun 2020 00:02:50: 49000000 INFO @ Tue, 30 Jun 2020 00:02:53: 44000000 INFO @ Tue, 30 Jun 2020 00:02:56: 50000000 INFO @ Tue, 30 Jun 2020 00:03:00: 45000000 INFO @ Tue, 30 Jun 2020 00:03:02: 51000000 INFO @ Tue, 30 Jun 2020 00:03:03: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 00:03:03: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 00:03:03: #1 total tags in treatment: 23628856 INFO @ Tue, 30 Jun 2020 00:03:03: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:03:03: #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 00:03:04: #1 tags after filtering in treatment: 17110447 INFO @ Tue, 30 Jun 2020 00:03:04: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 30 Jun 2020 00:03:04: #1 finished! INFO @ Tue, 30 Jun 2020 00:03:04: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:03:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:03:05: #2 number of paired peaks: 41 WARNING @ Tue, 30 Jun 2020 00:03:05: Too few paired peaks (41) 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 00:03:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1704844/SRX1704844.10_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/SRX1704844/SRX1704844.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1704844/SRX1704844.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1704844/SRX1704844.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:03:07: 46000000 INFO @ Tue, 30 Jun 2020 00:03:14: 47000000 INFO @ Tue, 30 Jun 2020 00:03:20: 48000000 INFO @ Tue, 30 Jun 2020 00:03:26: 49000000 INFO @ Tue, 30 Jun 2020 00:03:33: 50000000 INFO @ Tue, 30 Jun 2020 00:03:39: 51000000 INFO @ Tue, 30 Jun 2020 00:03:40: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 00:03:40: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 00:03:40: #1 total tags in treatment: 23628856 INFO @ Tue, 30 Jun 2020 00:03:40: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:03:40: #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 00:03:40: #1 tags after filtering in treatment: 17110447 INFO @ Tue, 30 Jun 2020 00:03:40: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 30 Jun 2020 00:03:40: #1 finished! INFO @ Tue, 30 Jun 2020 00:03:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:03:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:03:41: #2 number of paired peaks: 41 WARNING @ Tue, 30 Jun 2020 00:03:41: Too few paired peaks (41) 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 00:03:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1704844/SRX1704844.20_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/SRX1704844/SRX1704844.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1704844/SRX1704844.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1704844/SRX1704844.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling