Job ID = 6527563 SRX = SRX1115696 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:59:23 prefetch.2.10.7: 1) Downloading 'SRR2124125'... 2020-06-29T12:59:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:01:51 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:01:51 prefetch.2.10.7: 1) 'SRR2124125' was downloaded successfully 2020-06-29T13:02:43 prefetch.2.10.7: 'SRR2124125' has 10 unresolved dependencies 2020-06-29T13:02:43 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.4?vdb-ctx=refseq'... 2020-06-29T13:02:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:02:58 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:02:58 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.4?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:02:58 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.5?vdb-ctx=refseq'... 2020-06-29T13:02:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:03:11 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:03:11 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.5?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:03:11 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.3?vdb-ctx=refseq'... 2020-06-29T13:03:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:03:20 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:03:20 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.3?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:03:20 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.4?vdb-ctx=refseq'... 2020-06-29T13:03:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:03:33 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:03:33 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.4?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:03:33 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.2?vdb-ctx=refseq'... 2020-06-29T13:03:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:03:49 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:03:49 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.2?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:03:49 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.4?vdb-ctx=refseq'... 2020-06-29T13:03:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:04:02 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:04:02 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.4?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:04:02 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CM000457.1?vdb-ctx=refseq'... 2020-06-29T13:04:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:04:16 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:04:16 prefetch.2.10.7: 8) 'ncbi-acc:CM000457.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:04:16 prefetch.2.10.7: 9) Downloading 'ncbi-acc:CM000458.1?vdb-ctx=refseq'... 2020-06-29T13:04:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:04:26 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:04:26 prefetch.2.10.7: 9) 'ncbi-acc:CM000458.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:04:26 prefetch.2.10.7: 10) Downloading 'ncbi-acc:CM000459.1?vdb-ctx=refseq'... 2020-06-29T13:04:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:04:34 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:04:34 prefetch.2.10.7: 10) 'ncbi-acc:CM000459.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:04:34 prefetch.2.10.7: 11) Downloading 'ncbi-acc:FA000001.1?vdb-ctx=refseq'... 2020-06-29T13:04:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:04:50 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:04:50 prefetch.2.10.7: 11) 'ncbi-acc:FA000001.1?vdb-ctx=refseq' was downloaded successfully Read 27652944 spots for SRR2124125/SRR2124125.sra Written 27652944 spots for SRR2124125/SRR2124125.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:09 27652944 reads; of these: 27652944 (100.00%) were unpaired; of these: 1428680 (5.17%) aligned 0 times 20030842 (72.44%) aligned exactly 1 time 6193422 (22.40%) aligned >1 times 94.83% overall alignment rate Time searching: 00:08:10 Overall time: 00:08:10 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_rmdupse_core] 2589954 / 26224264 = 0.0988 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 22:29:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1115696/SRX1115696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1115696/SRX1115696.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1115696/SRX1115696.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1115696/SRX1115696.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 22:29:09: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:29:09: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:29:15: 1000000 INFO @ Mon, 29 Jun 2020 22:29:21: 2000000 INFO @ Mon, 29 Jun 2020 22:29:26: 3000000 INFO @ Mon, 29 Jun 2020 22:29:32: 4000000 INFO @ Mon, 29 Jun 2020 22:29:37: 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 22:29:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1115696/SRX1115696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1115696/SRX1115696.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1115696/SRX1115696.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1115696/SRX1115696.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 22:29:39: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:29:39: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:29:43: 6000000 INFO @ Mon, 29 Jun 2020 22:29:46: 1000000 INFO @ Mon, 29 Jun 2020 22:29:49: 7000000 INFO @ Mon, 29 Jun 2020 22:29:52: 2000000 INFO @ Mon, 29 Jun 2020 22:29:55: 8000000 INFO @ Mon, 29 Jun 2020 22:29:58: 3000000 INFO @ Mon, 29 Jun 2020 22:30:01: 9000000 INFO @ Mon, 29 Jun 2020 22:30:04: 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 22:30:07: 10000000 INFO @ Mon, 29 Jun 2020 22:30:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1115696/SRX1115696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1115696/SRX1115696.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1115696/SRX1115696.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1115696/SRX1115696.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 22:30:09: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:30:09: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:30:10: 5000000 INFO @ Mon, 29 Jun 2020 22:30:13: 11000000 INFO @ Mon, 29 Jun 2020 22:30:16: 1000000 INFO @ Mon, 29 Jun 2020 22:30:17: 6000000 INFO @ Mon, 29 Jun 2020 22:30:19: 12000000 INFO @ Mon, 29 Jun 2020 22:30:22: 2000000 INFO @ Mon, 29 Jun 2020 22:30:23: 7000000 INFO @ Mon, 29 Jun 2020 22:30:26: 13000000 INFO @ Mon, 29 Jun 2020 22:30:28: 3000000 INFO @ Mon, 29 Jun 2020 22:30:29: 8000000 INFO @ Mon, 29 Jun 2020 22:30:32: 14000000 INFO @ Mon, 29 Jun 2020 22:30:34: 4000000 INFO @ Mon, 29 Jun 2020 22:30:35: 9000000 INFO @ Mon, 29 Jun 2020 22:30:38: 15000000 INFO @ Mon, 29 Jun 2020 22:30:39: 5000000 INFO @ Mon, 29 Jun 2020 22:30:41: 10000000 INFO @ Mon, 29 Jun 2020 22:30:44: 16000000 INFO @ Mon, 29 Jun 2020 22:30:45: 6000000 INFO @ Mon, 29 Jun 2020 22:30:47: 11000000 INFO @ Mon, 29 Jun 2020 22:30:50: 17000000 INFO @ Mon, 29 Jun 2020 22:30:51: 7000000 INFO @ Mon, 29 Jun 2020 22:30:53: 12000000 INFO @ Mon, 29 Jun 2020 22:30:56: 18000000 INFO @ Mon, 29 Jun 2020 22:30:57: 8000000 INFO @ Mon, 29 Jun 2020 22:30:59: 13000000 INFO @ Mon, 29 Jun 2020 22:31:03: 19000000 INFO @ Mon, 29 Jun 2020 22:31:04: 9000000 INFO @ Mon, 29 Jun 2020 22:31:06: 14000000 INFO @ Mon, 29 Jun 2020 22:31:09: 20000000 INFO @ Mon, 29 Jun 2020 22:31:10: 10000000 INFO @ Mon, 29 Jun 2020 22:31:12: 15000000 INFO @ Mon, 29 Jun 2020 22:31:15: 11000000 INFO @ Mon, 29 Jun 2020 22:31:15: 21000000 INFO @ Mon, 29 Jun 2020 22:31:18: 16000000 INFO @ Mon, 29 Jun 2020 22:31:21: 12000000 INFO @ Mon, 29 Jun 2020 22:31:21: 22000000 INFO @ Mon, 29 Jun 2020 22:31:24: 17000000 INFO @ Mon, 29 Jun 2020 22:31:27: 13000000 INFO @ Mon, 29 Jun 2020 22:31:27: 23000000 INFO @ Mon, 29 Jun 2020 22:31:30: 18000000 INFO @ Mon, 29 Jun 2020 22:31:31: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 22:31:31: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 22:31:31: #1 total tags in treatment: 23634310 INFO @ Mon, 29 Jun 2020 22:31:31: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:31:31: #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 22:31:32: #1 tags after filtering in treatment: 23634310 INFO @ Mon, 29 Jun 2020 22:31:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:31:32: #1 finished! INFO @ Mon, 29 Jun 2020 22:31:32: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:31:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:31:33: 14000000 INFO @ Mon, 29 Jun 2020 22:31:33: #2 number of paired peaks: 39 WARNING @ Mon, 29 Jun 2020 22:31:33: Too few paired peaks (39) 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 22:31:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1115696/SRX1115696.05_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/SRX1115696/SRX1115696.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1115696/SRX1115696.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1115696/SRX1115696.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:31:35: 19000000 INFO @ Mon, 29 Jun 2020 22:31:39: 15000000 INFO @ Mon, 29 Jun 2020 22:31:41: 20000000 INFO @ Mon, 29 Jun 2020 22:31:45: 16000000 INFO @ Mon, 29 Jun 2020 22:31:46: 21000000 INFO @ Mon, 29 Jun 2020 22:31:51: 17000000 INFO @ Mon, 29 Jun 2020 22:31:52: 22000000 INFO @ Mon, 29 Jun 2020 22:31:57: 23000000 INFO @ Mon, 29 Jun 2020 22:31:57: 18000000 INFO @ Mon, 29 Jun 2020 22:32:01: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 22:32:01: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 22:32:01: #1 total tags in treatment: 23634310 INFO @ Mon, 29 Jun 2020 22:32:01: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:32:01: #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 22:32:01: #1 tags after filtering in treatment: 23634310 INFO @ Mon, 29 Jun 2020 22:32:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:32:01: #1 finished! INFO @ Mon, 29 Jun 2020 22:32:01: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:32:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:32:03: #2 number of paired peaks: 39 WARNING @ Mon, 29 Jun 2020 22:32:03: Too few paired peaks (39) 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 22:32:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1115696/SRX1115696.10_peaks.narrowPeak: No such file or directory INFO @ Mon, 29 Jun 2020 22:32:03: 19000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1115696/SRX1115696.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1115696/SRX1115696.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1115696/SRX1115696.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:32:08: 20000000 INFO @ Mon, 29 Jun 2020 22:32:14: 21000000 INFO @ Mon, 29 Jun 2020 22:32:19: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:32:25: 23000000 INFO @ Mon, 29 Jun 2020 22:32:29: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 22:32:29: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 22:32:29: #1 total tags in treatment: 23634310 INFO @ Mon, 29 Jun 2020 22:32:29: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:32:29: #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 22:32:29: #1 tags after filtering in treatment: 23634310 INFO @ Mon, 29 Jun 2020 22:32:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:32:29: #1 finished! INFO @ Mon, 29 Jun 2020 22:32:29: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:32:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:32:31: #2 number of paired peaks: 39 WARNING @ Mon, 29 Jun 2020 22:32:31: Too few paired peaks (39) 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 22:32:31: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1115696/SRX1115696.20_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/SRX1115696/SRX1115696.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1115696/SRX1115696.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1115696/SRX1115696.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。