Job ID = 6527694 SRX = SRX2325639 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T12:58:23 prefetch.2.10.7: 1) Downloading 'SRR4896327'... 2020-06-29T12:58:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:01:58 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:01:58 prefetch.2.10.7: 1) 'SRR4896327' was downloaded successfully 2020-06-29T13:01:58 prefetch.2.10.7: 'SRR4896327' has 0 unresolved dependencies Read 22172408 spots for SRR4896327/SRR4896327.sra Written 22172408 spots for SRR4896327/SRR4896327.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: 00:50:03 22172408 reads; of these: 22172408 (100.00%) were paired; of these: 2407375 (10.86%) aligned concordantly 0 times 16402664 (73.98%) aligned concordantly exactly 1 time 3362369 (15.16%) aligned concordantly >1 times ---- 2407375 pairs aligned concordantly 0 times; of these: 413674 (17.18%) aligned discordantly 1 time ---- 1993701 pairs aligned 0 times concordantly or discordantly; of these: 3987402 mates make up the pairs; of these: 3038375 (76.20%) aligned 0 times 473730 (11.88%) aligned exactly 1 time 475297 (11.92%) aligned >1 times 93.15% overall alignment rate Time searching: 00:50:03 Overall time: 00:50:03 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 20 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] 875371 / 20117344 = 0.0435 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 23:30:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2325639/SRX2325639.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2325639/SRX2325639.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2325639/SRX2325639.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2325639/SRX2325639.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 23:30:57: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:30:57: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:31:06: 1000000 INFO @ Mon, 29 Jun 2020 23:31:14: 2000000 INFO @ Mon, 29 Jun 2020 23:31:23: 3000000 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 23:31:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2325639/SRX2325639.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2325639/SRX2325639.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2325639/SRX2325639.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2325639/SRX2325639.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 23:31:26: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:31:26: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:31:32: 4000000 INFO @ Mon, 29 Jun 2020 23:31:35: 1000000 INFO @ Mon, 29 Jun 2020 23:31:41: 5000000 INFO @ Mon, 29 Jun 2020 23:31:44: 2000000 INFO @ Mon, 29 Jun 2020 23:31:50: 6000000 INFO @ Mon, 29 Jun 2020 23:31:53: 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 23:31:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2325639/SRX2325639.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2325639/SRX2325639.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2325639/SRX2325639.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2325639/SRX2325639.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 23:31:56: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:31:56: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:31:59: 7000000 INFO @ Mon, 29 Jun 2020 23:32:02: 4000000 INFO @ Mon, 29 Jun 2020 23:32:06: 1000000 INFO @ Mon, 29 Jun 2020 23:32:08: 8000000 INFO @ Mon, 29 Jun 2020 23:32:11: 5000000 INFO @ Mon, 29 Jun 2020 23:32:15: 2000000 INFO @ Mon, 29 Jun 2020 23:32:18: 9000000 INFO @ Mon, 29 Jun 2020 23:32:20: 6000000 INFO @ Mon, 29 Jun 2020 23:32:24: 3000000 INFO @ Mon, 29 Jun 2020 23:32:27: 10000000 INFO @ Mon, 29 Jun 2020 23:32:29: 7000000 INFO @ Mon, 29 Jun 2020 23:32:34: 4000000 INFO @ Mon, 29 Jun 2020 23:32:36: 11000000 INFO @ Mon, 29 Jun 2020 23:32:38: 8000000 INFO @ Mon, 29 Jun 2020 23:32:43: 5000000 INFO @ Mon, 29 Jun 2020 23:32:46: 12000000 INFO @ Mon, 29 Jun 2020 23:32:47: 9000000 INFO @ Mon, 29 Jun 2020 23:32:51: 6000000 INFO @ Mon, 29 Jun 2020 23:32:56: 10000000 INFO @ Mon, 29 Jun 2020 23:32:56: 13000000 INFO @ Mon, 29 Jun 2020 23:33:00: 7000000 INFO @ Mon, 29 Jun 2020 23:33:05: 11000000 INFO @ Mon, 29 Jun 2020 23:33:06: 14000000 INFO @ Mon, 29 Jun 2020 23:33:09: 8000000 INFO @ Mon, 29 Jun 2020 23:33:13: 12000000 INFO @ Mon, 29 Jun 2020 23:33:15: 15000000 INFO @ Mon, 29 Jun 2020 23:33:18: 9000000 INFO @ Mon, 29 Jun 2020 23:33:22: 13000000 INFO @ Mon, 29 Jun 2020 23:33:24: 16000000 INFO @ Mon, 29 Jun 2020 23:33:27: 10000000 INFO @ Mon, 29 Jun 2020 23:33:31: 14000000 INFO @ Mon, 29 Jun 2020 23:33:33: 17000000 INFO @ Mon, 29 Jun 2020 23:33:36: 11000000 INFO @ Mon, 29 Jun 2020 23:33:40: 15000000 INFO @ Mon, 29 Jun 2020 23:33:42: 18000000 INFO @ Mon, 29 Jun 2020 23:33:45: 12000000 INFO @ Mon, 29 Jun 2020 23:33:49: 16000000 INFO @ Mon, 29 Jun 2020 23:33:51: 19000000 INFO @ Mon, 29 Jun 2020 23:33:54: 13000000 INFO @ Mon, 29 Jun 2020 23:33:58: 17000000 INFO @ Mon, 29 Jun 2020 23:34:01: 20000000 INFO @ Mon, 29 Jun 2020 23:34:03: 14000000 INFO @ Mon, 29 Jun 2020 23:34:08: 18000000 INFO @ Mon, 29 Jun 2020 23:34:10: 21000000 INFO @ Mon, 29 Jun 2020 23:34:12: 15000000 INFO @ Mon, 29 Jun 2020 23:34:16: 19000000 INFO @ Mon, 29 Jun 2020 23:34:19: 22000000 INFO @ Mon, 29 Jun 2020 23:34:21: 16000000 INFO @ Mon, 29 Jun 2020 23:34:25: 20000000 INFO @ Mon, 29 Jun 2020 23:34:28: 23000000 INFO @ Mon, 29 Jun 2020 23:34:30: 17000000 INFO @ Mon, 29 Jun 2020 23:34:34: 21000000 INFO @ Mon, 29 Jun 2020 23:34:37: 24000000 INFO @ Mon, 29 Jun 2020 23:34:39: 18000000 INFO @ Mon, 29 Jun 2020 23:34:44: 22000000 INFO @ Mon, 29 Jun 2020 23:34:47: 25000000 INFO @ Mon, 29 Jun 2020 23:34:48: 19000000 INFO @ Mon, 29 Jun 2020 23:34:53: 23000000 INFO @ Mon, 29 Jun 2020 23:34:56: 26000000 INFO @ Mon, 29 Jun 2020 23:34:57: 20000000 INFO @ Mon, 29 Jun 2020 23:35:02: 24000000 INFO @ Mon, 29 Jun 2020 23:35:05: 27000000 INFO @ Mon, 29 Jun 2020 23:35:06: 21000000 INFO @ Mon, 29 Jun 2020 23:35:11: 25000000 INFO @ Mon, 29 Jun 2020 23:35:14: 28000000 INFO @ Mon, 29 Jun 2020 23:35:15: 22000000 INFO @ Mon, 29 Jun 2020 23:35:20: 26000000 INFO @ Mon, 29 Jun 2020 23:35:23: 29000000 INFO @ Mon, 29 Jun 2020 23:35:24: 23000000 INFO @ Mon, 29 Jun 2020 23:35:29: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:35:32: 30000000 INFO @ Mon, 29 Jun 2020 23:35:33: 24000000 INFO @ Mon, 29 Jun 2020 23:35:38: 28000000 INFO @ Mon, 29 Jun 2020 23:35:41: 31000000 INFO @ Mon, 29 Jun 2020 23:35:42: 25000000 INFO @ Mon, 29 Jun 2020 23:35:47: 29000000 INFO @ Mon, 29 Jun 2020 23:35:51: 32000000 INFO @ Mon, 29 Jun 2020 23:35:51: 26000000 INFO @ Mon, 29 Jun 2020 23:35:56: 30000000 INFO @ Mon, 29 Jun 2020 23:36:00: 27000000 INFO @ Mon, 29 Jun 2020 23:36:00: 33000000 INFO @ Mon, 29 Jun 2020 23:36:05: 31000000 INFO @ Mon, 29 Jun 2020 23:36:09: 28000000 INFO @ Mon, 29 Jun 2020 23:36:10: 34000000 INFO @ Mon, 29 Jun 2020 23:36:14: 32000000 INFO @ Mon, 29 Jun 2020 23:36:17: 29000000 INFO @ Mon, 29 Jun 2020 23:36:20: 35000000 INFO @ Mon, 29 Jun 2020 23:36:23: 33000000 INFO @ Mon, 29 Jun 2020 23:36:26: 30000000 INFO @ Mon, 29 Jun 2020 23:36:29: 36000000 INFO @ Mon, 29 Jun 2020 23:36:33: 34000000 INFO @ Mon, 29 Jun 2020 23:36:35: 31000000 INFO @ Mon, 29 Jun 2020 23:36:39: 37000000 INFO @ Mon, 29 Jun 2020 23:36:43: 35000000 INFO @ Mon, 29 Jun 2020 23:36:44: 32000000 INFO @ Mon, 29 Jun 2020 23:36:49: 38000000 INFO @ Mon, 29 Jun 2020 23:36:53: 36000000 INFO @ Mon, 29 Jun 2020 23:36:53: 33000000 INFO @ Mon, 29 Jun 2020 23:36:58: 39000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:37:02: 37000000 INFO @ Mon, 29 Jun 2020 23:37:03: 34000000 INFO @ Mon, 29 Jun 2020 23:37:03: #1 tag size is determined as 76 bps INFO @ Mon, 29 Jun 2020 23:37:03: #1 tag size = 76 INFO @ Mon, 29 Jun 2020 23:37:03: #1 total tags in treatment: 18898449 INFO @ Mon, 29 Jun 2020 23:37:03: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:37:03: #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 23:37:04: #1 tags after filtering in treatment: 17543939 INFO @ Mon, 29 Jun 2020 23:37:04: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 29 Jun 2020 23:37:04: #1 finished! INFO @ Mon, 29 Jun 2020 23:37:04: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:37:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:37:05: #2 number of paired peaks: 59 WARNING @ Mon, 29 Jun 2020 23:37:05: Too few paired peaks (59) 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 23:37:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX2325639/SRX2325639.05_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/SRX2325639/SRX2325639.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2325639/SRX2325639.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2325639/SRX2325639.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:37:11: 38000000 INFO @ Mon, 29 Jun 2020 23:37:12: 35000000 INFO @ Mon, 29 Jun 2020 23:37:20: 39000000 INFO @ Mon, 29 Jun 2020 23:37:22: 36000000 INFO @ Mon, 29 Jun 2020 23:37:25: #1 tag size is determined as 76 bps INFO @ Mon, 29 Jun 2020 23:37:25: #1 tag size = 76 INFO @ Mon, 29 Jun 2020 23:37:25: #1 total tags in treatment: 18898449 INFO @ Mon, 29 Jun 2020 23:37:25: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:37:25: #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 23:37:26: #1 tags after filtering in treatment: 17543939 INFO @ Mon, 29 Jun 2020 23:37:26: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 29 Jun 2020 23:37:26: #1 finished! INFO @ Mon, 29 Jun 2020 23:37:26: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:37:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:37:27: #2 number of paired peaks: 59 WARNING @ Mon, 29 Jun 2020 23:37:27: Too few paired peaks (59) 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 23:37:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX2325639/SRX2325639.10_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/SRX2325639/SRX2325639.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2325639/SRX2325639.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2325639/SRX2325639.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:37:30: 37000000 INFO @ Mon, 29 Jun 2020 23:37:39: 38000000 INFO @ Mon, 29 Jun 2020 23:37:47: 39000000 INFO @ Mon, 29 Jun 2020 23:37:51: #1 tag size is determined as 76 bps INFO @ Mon, 29 Jun 2020 23:37:51: #1 tag size = 76 INFO @ Mon, 29 Jun 2020 23:37:51: #1 total tags in treatment: 18898449 INFO @ Mon, 29 Jun 2020 23:37:51: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:37:51: #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 23:37:52: #1 tags after filtering in treatment: 17543939 INFO @ Mon, 29 Jun 2020 23:37:52: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 29 Jun 2020 23:37:52: #1 finished! INFO @ Mon, 29 Jun 2020 23:37:52: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:37:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:37:53: #2 number of paired peaks: 59 WARNING @ Mon, 29 Jun 2020 23:37:53: Too few paired peaks (59) 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 23:37:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX2325639/SRX2325639.20_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/SRX2325639/SRX2325639.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2325639/SRX2325639.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2325639/SRX2325639.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling