Job ID = 6527439 SRX = ERX2075303 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T12:43:31 prefetch.2.10.7: 1) Downloading 'ERR2015721'... 2020-06-29T12:43:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:52:08 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:52:08 prefetch.2.10.7: 1) 'ERR2015721' was downloaded successfully Read 29786549 spots for ERR2015721/ERR2015721.sra Written 29786549 spots for ERR2015721/ERR2015721.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: 01:06:38 29786549 reads; of these: 29786549 (100.00%) were paired; of these: 3046303 (10.23%) aligned concordantly 0 times 20218313 (67.88%) aligned concordantly exactly 1 time 6521933 (21.90%) aligned concordantly >1 times ---- 3046303 pairs aligned concordantly 0 times; of these: 636070 (20.88%) aligned discordantly 1 time ---- 2410233 pairs aligned 0 times concordantly or discordantly; of these: 4820466 mates make up the pairs; of these: 3299513 (68.45%) aligned 0 times 867860 (18.00%) aligned exactly 1 time 653093 (13.55%) aligned >1 times 94.46% overall alignment rate Time searching: 01:06:38 Overall time: 01:06:38 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] 1195094 / 27080140 = 0.0441 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 23:32:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2075303/ERX2075303.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2075303/ERX2075303.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2075303/ERX2075303.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2075303/ERX2075303.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 23:32:11: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:32:11: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:32:17: 1000000 INFO @ Mon, 29 Jun 2020 23:32:22: 2000000 INFO @ Mon, 29 Jun 2020 23:32:28: 3000000 INFO @ Mon, 29 Jun 2020 23:32:34: 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 23:32:40: 5000000 INFO @ Mon, 29 Jun 2020 23:32:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2075303/ERX2075303.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2075303/ERX2075303.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2075303/ERX2075303.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2075303/ERX2075303.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 23:32:41: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:32:41: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:32:47: 6000000 INFO @ Mon, 29 Jun 2020 23:32:49: 1000000 INFO @ Mon, 29 Jun 2020 23:32:54: 7000000 INFO @ Mon, 29 Jun 2020 23:32:57: 2000000 INFO @ Mon, 29 Jun 2020 23:33:02: 8000000 INFO @ Mon, 29 Jun 2020 23:33:04: 3000000 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 23:33:09: 9000000 INFO @ Mon, 29 Jun 2020 23:33:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2075303/ERX2075303.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2075303/ERX2075303.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2075303/ERX2075303.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2075303/ERX2075303.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 23:33:11: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:33:11: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:33:12: 4000000 INFO @ Mon, 29 Jun 2020 23:33:17: 10000000 INFO @ Mon, 29 Jun 2020 23:33:18: 1000000 INFO @ Mon, 29 Jun 2020 23:33:20: 5000000 INFO @ Mon, 29 Jun 2020 23:33:24: 11000000 INFO @ Mon, 29 Jun 2020 23:33:26: 2000000 INFO @ Mon, 29 Jun 2020 23:33:28: 6000000 INFO @ Mon, 29 Jun 2020 23:33:32: 12000000 INFO @ Mon, 29 Jun 2020 23:33:33: 3000000 INFO @ Mon, 29 Jun 2020 23:33:36: 7000000 INFO @ Mon, 29 Jun 2020 23:33:39: 13000000 INFO @ Mon, 29 Jun 2020 23:33:41: 4000000 INFO @ Mon, 29 Jun 2020 23:33:44: 8000000 INFO @ Mon, 29 Jun 2020 23:33:47: 14000000 INFO @ Mon, 29 Jun 2020 23:33:49: 5000000 INFO @ Mon, 29 Jun 2020 23:33:51: 9000000 INFO @ Mon, 29 Jun 2020 23:33:55: 15000000 INFO @ Mon, 29 Jun 2020 23:33:56: 6000000 INFO @ Mon, 29 Jun 2020 23:33:59: 10000000 INFO @ Mon, 29 Jun 2020 23:34:02: 16000000 INFO @ Mon, 29 Jun 2020 23:34:04: 7000000 INFO @ Mon, 29 Jun 2020 23:34:07: 11000000 INFO @ Mon, 29 Jun 2020 23:34:10: 17000000 INFO @ Mon, 29 Jun 2020 23:34:11: 8000000 INFO @ Mon, 29 Jun 2020 23:34:15: 12000000 INFO @ Mon, 29 Jun 2020 23:34:17: 18000000 INFO @ Mon, 29 Jun 2020 23:34:19: 9000000 INFO @ Mon, 29 Jun 2020 23:34:23: 13000000 INFO @ Mon, 29 Jun 2020 23:34:25: 19000000 INFO @ Mon, 29 Jun 2020 23:34:26: 10000000 INFO @ Mon, 29 Jun 2020 23:34:30: 14000000 INFO @ Mon, 29 Jun 2020 23:34:33: 20000000 INFO @ Mon, 29 Jun 2020 23:34:34: 11000000 INFO @ Mon, 29 Jun 2020 23:34:38: 15000000 INFO @ Mon, 29 Jun 2020 23:34:40: 21000000 INFO @ Mon, 29 Jun 2020 23:34:41: 12000000 INFO @ Mon, 29 Jun 2020 23:34:46: 16000000 INFO @ Mon, 29 Jun 2020 23:34:48: 22000000 INFO @ Mon, 29 Jun 2020 23:34:49: 13000000 INFO @ Mon, 29 Jun 2020 23:34:54: 17000000 INFO @ Mon, 29 Jun 2020 23:34:56: 23000000 INFO @ Mon, 29 Jun 2020 23:34:57: 14000000 INFO @ Mon, 29 Jun 2020 23:35:02: 18000000 INFO @ Mon, 29 Jun 2020 23:35:04: 24000000 INFO @ Mon, 29 Jun 2020 23:35:05: 15000000 INFO @ Mon, 29 Jun 2020 23:35:11: 19000000 INFO @ Mon, 29 Jun 2020 23:35:12: 25000000 INFO @ Mon, 29 Jun 2020 23:35:13: 16000000 INFO @ Mon, 29 Jun 2020 23:35:19: 20000000 INFO @ Mon, 29 Jun 2020 23:35:19: 26000000 INFO @ Mon, 29 Jun 2020 23:35:21: 17000000 INFO @ Mon, 29 Jun 2020 23:35:27: 21000000 INFO @ Mon, 29 Jun 2020 23:35:27: 27000000 INFO @ Mon, 29 Jun 2020 23:35:29: 18000000 INFO @ Mon, 29 Jun 2020 23:35:35: 28000000 INFO @ Mon, 29 Jun 2020 23:35:35: 22000000 INFO @ Mon, 29 Jun 2020 23:35:37: 19000000 INFO @ Mon, 29 Jun 2020 23:35:43: 29000000 INFO @ Mon, 29 Jun 2020 23:35:43: 23000000 INFO @ Mon, 29 Jun 2020 23:35:45: 20000000 INFO @ Mon, 29 Jun 2020 23:35:51: 24000000 INFO @ Mon, 29 Jun 2020 23:35:51: 30000000 INFO @ Mon, 29 Jun 2020 23:35:53: 21000000 INFO @ Mon, 29 Jun 2020 23:35:59: 25000000 INFO @ Mon, 29 Jun 2020 23:35:59: 31000000 INFO @ Mon, 29 Jun 2020 23:36:01: 22000000 INFO @ Mon, 29 Jun 2020 23:36:07: 26000000 INFO @ Mon, 29 Jun 2020 23:36:07: 32000000 INFO @ Mon, 29 Jun 2020 23:36:08: 23000000 INFO @ Mon, 29 Jun 2020 23:36:14: 33000000 INFO @ Mon, 29 Jun 2020 23:36:15: 27000000 INFO @ Mon, 29 Jun 2020 23:36:16: 24000000 INFO @ Mon, 29 Jun 2020 23:36:22: 34000000 INFO @ Mon, 29 Jun 2020 23:36:23: 28000000 INFO @ Mon, 29 Jun 2020 23:36:24: 25000000 INFO @ Mon, 29 Jun 2020 23:36:29: 35000000 INFO @ Mon, 29 Jun 2020 23:36:31: 29000000 INFO @ Mon, 29 Jun 2020 23:36:31: 26000000 INFO @ Mon, 29 Jun 2020 23:36:37: 36000000 INFO @ Mon, 29 Jun 2020 23:36:39: 27000000 INFO @ Mon, 29 Jun 2020 23:36:39: 30000000 INFO @ Mon, 29 Jun 2020 23:36:44: 37000000 INFO @ Mon, 29 Jun 2020 23:36:47: 28000000 INFO @ Mon, 29 Jun 2020 23:36:47: 31000000 INFO @ Mon, 29 Jun 2020 23:36:52: 38000000 INFO @ Mon, 29 Jun 2020 23:36:54: 29000000 INFO @ Mon, 29 Jun 2020 23:36:55: 32000000 INFO @ Mon, 29 Jun 2020 23:36:59: 39000000 INFO @ Mon, 29 Jun 2020 23:37:02: 30000000 INFO @ Mon, 29 Jun 2020 23:37:03: 33000000 INFO @ Mon, 29 Jun 2020 23:37:06: 40000000 INFO @ Mon, 29 Jun 2020 23:37:09: 31000000 INFO @ Mon, 29 Jun 2020 23:37:11: 34000000 INFO @ Mon, 29 Jun 2020 23:37:14: 41000000 INFO @ Mon, 29 Jun 2020 23:37:17: 32000000 INFO @ Mon, 29 Jun 2020 23:37:19: 35000000 INFO @ Mon, 29 Jun 2020 23:37:22: 42000000 INFO @ Mon, 29 Jun 2020 23:37:25: 33000000 INFO @ Mon, 29 Jun 2020 23:37:27: 36000000 INFO @ Mon, 29 Jun 2020 23:37:30: 43000000 INFO @ Mon, 29 Jun 2020 23:37:32: 34000000 INFO @ Mon, 29 Jun 2020 23:37:35: 37000000 INFO @ Mon, 29 Jun 2020 23:37:37: 44000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:37:40: 35000000 INFO @ Mon, 29 Jun 2020 23:37:43: 38000000 INFO @ Mon, 29 Jun 2020 23:37:45: 45000000 INFO @ Mon, 29 Jun 2020 23:37:48: 36000000 INFO @ Mon, 29 Jun 2020 23:37:51: 39000000 INFO @ Mon, 29 Jun 2020 23:37:53: 46000000 INFO @ Mon, 29 Jun 2020 23:37:55: 37000000 INFO @ Mon, 29 Jun 2020 23:37:59: 40000000 INFO @ Mon, 29 Jun 2020 23:38:00: 47000000 INFO @ Mon, 29 Jun 2020 23:38:03: 38000000 INFO @ Mon, 29 Jun 2020 23:38:08: 48000000 INFO @ Mon, 29 Jun 2020 23:38:08: 41000000 INFO @ Mon, 29 Jun 2020 23:38:10: 39000000 INFO @ Mon, 29 Jun 2020 23:38:15: 49000000 INFO @ Mon, 29 Jun 2020 23:38:16: 42000000 INFO @ Mon, 29 Jun 2020 23:38:18: 40000000 INFO @ Mon, 29 Jun 2020 23:38:23: 50000000 INFO @ Mon, 29 Jun 2020 23:38:24: 43000000 INFO @ Mon, 29 Jun 2020 23:38:26: 41000000 INFO @ Mon, 29 Jun 2020 23:38:30: 51000000 INFO @ Mon, 29 Jun 2020 23:38:32: 44000000 INFO @ Mon, 29 Jun 2020 23:38:34: 42000000 INFO @ Mon, 29 Jun 2020 23:38:38: 52000000 INFO @ Mon, 29 Jun 2020 23:38:41: 45000000 INFO @ Mon, 29 Jun 2020 23:38:41: 43000000 INFO @ Mon, 29 Jun 2020 23:38:45: 53000000 INFO @ Mon, 29 Jun 2020 23:38:49: 44000000 INFO @ Mon, 29 Jun 2020 23:38:49: 46000000 INFO @ Mon, 29 Jun 2020 23:38:52: #1 tag size is determined as 75 bps INFO @ Mon, 29 Jun 2020 23:38:52: #1 tag size = 75 INFO @ Mon, 29 Jun 2020 23:38:52: #1 total tags in treatment: 25556810 INFO @ Mon, 29 Jun 2020 23:38:52: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:38:52: #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 23:38:52: #1 tags after filtering in treatment: 23739887 INFO @ Mon, 29 Jun 2020 23:38:52: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 29 Jun 2020 23:38:52: #1 finished! INFO @ Mon, 29 Jun 2020 23:38:52: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:38:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:38:54: #2 number of paired peaks: 54 WARNING @ Mon, 29 Jun 2020 23:38:54: Too few paired peaks (54) 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 23:38:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/ERX2075303/ERX2075303.05_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/ERX2075303/ERX2075303.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX2075303/ERX2075303.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX2075303/ERX2075303.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:38:56: 45000000 INFO @ Mon, 29 Jun 2020 23:38:57: 47000000 INFO @ Mon, 29 Jun 2020 23:39:03: 46000000 INFO @ Mon, 29 Jun 2020 23:39:05: 48000000 INFO @ Mon, 29 Jun 2020 23:39:11: 47000000 INFO @ Mon, 29 Jun 2020 23:39:14: 49000000 INFO @ Mon, 29 Jun 2020 23:39:18: 48000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:39:22: 50000000 INFO @ Mon, 29 Jun 2020 23:39:26: 49000000 INFO @ Mon, 29 Jun 2020 23:39:30: 51000000 INFO @ Mon, 29 Jun 2020 23:39:33: 50000000 INFO @ Mon, 29 Jun 2020 23:39:39: 52000000 INFO @ Mon, 29 Jun 2020 23:39:40: 51000000 INFO @ Mon, 29 Jun 2020 23:39:47: 53000000 INFO @ Mon, 29 Jun 2020 23:39:48: 52000000 INFO @ Mon, 29 Jun 2020 23:39:54: #1 tag size is determined as 75 bps INFO @ Mon, 29 Jun 2020 23:39:54: #1 tag size = 75 INFO @ Mon, 29 Jun 2020 23:39:54: #1 total tags in treatment: 25556810 INFO @ Mon, 29 Jun 2020 23:39:54: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:39:54: #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 23:39:55: #1 tags after filtering in treatment: 23739887 INFO @ Mon, 29 Jun 2020 23:39:55: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 29 Jun 2020 23:39:55: #1 finished! INFO @ Mon, 29 Jun 2020 23:39:55: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:39:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:39:55: 53000000 INFO @ Mon, 29 Jun 2020 23:39:56: #2 number of paired peaks: 54 WARNING @ Mon, 29 Jun 2020 23:39:56: Too few paired peaks (54) 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 23:39:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/ERX2075303/ERX2075303.10_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/ERX2075303/ERX2075303.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX2075303/ERX2075303.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX2075303/ERX2075303.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:40:01: #1 tag size is determined as 75 bps INFO @ Mon, 29 Jun 2020 23:40:01: #1 tag size = 75 INFO @ Mon, 29 Jun 2020 23:40:01: #1 total tags in treatment: 25556810 INFO @ Mon, 29 Jun 2020 23:40:01: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:40:01: #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 23:40:01: #1 tags after filtering in treatment: 23739887 INFO @ Mon, 29 Jun 2020 23:40:01: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 29 Jun 2020 23:40:01: #1 finished! INFO @ Mon, 29 Jun 2020 23:40:01: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:40:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:40:03: #2 number of paired peaks: 54 WARNING @ Mon, 29 Jun 2020 23:40:03: Too few paired peaks (54) 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 23:40:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/ERX2075303/ERX2075303.20_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/ERX2075303/ERX2075303.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX2075303/ERX2075303.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX2075303/ERX2075303.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling