Job ID = 5790629 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 123,810,851 reads read : 123,810,851 reads written : 123,810,851 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR125735.sra.cache’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:03 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:02 Multiseed full-index search: 01:01:17 123810851 reads; of these: 123810851 (100.00%) were unpaired; of these: 2205436 (1.78%) aligned 0 times 108192503 (87.39%) aligned exactly 1 time 13412912 (10.83%) aligned >1 times 98.22% overall alignment rate Time searching: 01:01:26 Overall time: 01:01:26 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 52 files... [bam_rmdupse_core] 72634504 / 121605415 = 0.5973 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 @ Wed, 22 Apr 2020 05:41:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 05:41:55: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:41:55: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:41:59: 1000000 INFO @ Wed, 22 Apr 2020 05:42:04: 2000000 INFO @ Wed, 22 Apr 2020 05:42:09: 3000000 INFO @ Wed, 22 Apr 2020 05:42:14: 4000000 INFO @ Wed, 22 Apr 2020 05:42:19: 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 @ Wed, 22 Apr 2020 05:42:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 05:42:23: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:42:23: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:42:24: 6000000 INFO @ Wed, 22 Apr 2020 05:42:28: 1000000 INFO @ Wed, 22 Apr 2020 05:42:29: 7000000 INFO @ Wed, 22 Apr 2020 05:42:33: 2000000 INFO @ Wed, 22 Apr 2020 05:42:34: 8000000 INFO @ Wed, 22 Apr 2020 05:42:38: 3000000 INFO @ Wed, 22 Apr 2020 05:42:39: 9000000 INFO @ Wed, 22 Apr 2020 05:42:43: 4000000 INFO @ Wed, 22 Apr 2020 05:42:44: 10000000 INFO @ Wed, 22 Apr 2020 05:42:48: 5000000 INFO @ Wed, 22 Apr 2020 05:42:49: 11000000 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 @ Wed, 22 Apr 2020 05:42:53: 6000000 INFO @ Wed, 22 Apr 2020 05:42:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 05:42:53: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:42:53: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:42:54: 12000000 INFO @ Wed, 22 Apr 2020 05:42:58: 7000000 INFO @ Wed, 22 Apr 2020 05:42:59: 13000000 INFO @ Wed, 22 Apr 2020 05:42:59: 1000000 INFO @ Wed, 22 Apr 2020 05:43:03: 8000000 INFO @ Wed, 22 Apr 2020 05:43:04: 14000000 INFO @ Wed, 22 Apr 2020 05:43:04: 2000000 INFO @ Wed, 22 Apr 2020 05:43:08: 9000000 INFO @ Wed, 22 Apr 2020 05:43:09: 15000000 INFO @ Wed, 22 Apr 2020 05:43:10: 3000000 INFO @ Wed, 22 Apr 2020 05:43:13: 10000000 INFO @ Wed, 22 Apr 2020 05:43:14: 16000000 INFO @ Wed, 22 Apr 2020 05:43:15: 4000000 INFO @ Wed, 22 Apr 2020 05:43:19: 11000000 INFO @ Wed, 22 Apr 2020 05:43:19: 17000000 INFO @ Wed, 22 Apr 2020 05:43:20: 5000000 INFO @ Wed, 22 Apr 2020 05:43:24: 12000000 INFO @ Wed, 22 Apr 2020 05:43:24: 18000000 INFO @ Wed, 22 Apr 2020 05:43:25: 6000000 INFO @ Wed, 22 Apr 2020 05:43:29: 13000000 INFO @ Wed, 22 Apr 2020 05:43:29: 19000000 INFO @ Wed, 22 Apr 2020 05:43:30: 7000000 INFO @ Wed, 22 Apr 2020 05:43:34: 14000000 INFO @ Wed, 22 Apr 2020 05:43:34: 20000000 INFO @ Wed, 22 Apr 2020 05:43:35: 8000000 INFO @ Wed, 22 Apr 2020 05:43:39: 15000000 INFO @ Wed, 22 Apr 2020 05:43:39: 21000000 INFO @ Wed, 22 Apr 2020 05:43:40: 9000000 INFO @ Wed, 22 Apr 2020 05:43:44: 16000000 INFO @ Wed, 22 Apr 2020 05:43:44: 22000000 INFO @ Wed, 22 Apr 2020 05:43:45: 10000000 INFO @ Wed, 22 Apr 2020 05:43:49: 17000000 INFO @ Wed, 22 Apr 2020 05:43:49: 23000000 INFO @ Wed, 22 Apr 2020 05:43:51: 11000000 INFO @ Wed, 22 Apr 2020 05:43:54: 18000000 INFO @ Wed, 22 Apr 2020 05:43:54: 24000000 INFO @ Wed, 22 Apr 2020 05:43:56: 12000000 INFO @ Wed, 22 Apr 2020 05:43:59: 19000000 INFO @ Wed, 22 Apr 2020 05:43:59: 25000000 INFO @ Wed, 22 Apr 2020 05:44:01: 13000000 INFO @ Wed, 22 Apr 2020 05:44:04: 26000000 INFO @ Wed, 22 Apr 2020 05:44:04: 20000000 INFO @ Wed, 22 Apr 2020 05:44:06: 14000000 INFO @ Wed, 22 Apr 2020 05:44:09: 27000000 INFO @ Wed, 22 Apr 2020 05:44:09: 21000000 INFO @ Wed, 22 Apr 2020 05:44:11: 15000000 INFO @ Wed, 22 Apr 2020 05:44:14: 28000000 INFO @ Wed, 22 Apr 2020 05:44:14: 22000000 INFO @ Wed, 22 Apr 2020 05:44:16: 16000000 INFO @ Wed, 22 Apr 2020 05:44:19: 29000000 INFO @ Wed, 22 Apr 2020 05:44:19: 23000000 INFO @ Wed, 22 Apr 2020 05:44:21: 17000000 INFO @ Wed, 22 Apr 2020 05:44:24: 30000000 INFO @ Wed, 22 Apr 2020 05:44:24: 24000000 INFO @ Wed, 22 Apr 2020 05:44:26: 18000000 INFO @ Wed, 22 Apr 2020 05:44:29: 31000000 INFO @ Wed, 22 Apr 2020 05:44:29: 25000000 INFO @ Wed, 22 Apr 2020 05:44:31: 19000000 INFO @ Wed, 22 Apr 2020 05:44:34: 32000000 INFO @ Wed, 22 Apr 2020 05:44:34: 26000000 INFO @ Wed, 22 Apr 2020 05:44:36: 20000000 INFO @ Wed, 22 Apr 2020 05:44:39: 33000000 INFO @ Wed, 22 Apr 2020 05:44:39: 27000000 INFO @ Wed, 22 Apr 2020 05:44:41: 21000000 INFO @ Wed, 22 Apr 2020 05:44:44: 34000000 INFO @ Wed, 22 Apr 2020 05:44:44: 28000000 INFO @ Wed, 22 Apr 2020 05:44:46: 22000000 INFO @ Wed, 22 Apr 2020 05:44:49: 35000000 INFO @ Wed, 22 Apr 2020 05:44:49: 29000000 INFO @ Wed, 22 Apr 2020 05:44:51: 23000000 INFO @ Wed, 22 Apr 2020 05:44:54: 36000000 INFO @ Wed, 22 Apr 2020 05:44:55: 30000000 INFO @ Wed, 22 Apr 2020 05:44:56: 24000000 INFO @ Wed, 22 Apr 2020 05:44:59: 37000000 INFO @ Wed, 22 Apr 2020 05:45:00: 31000000 INFO @ Wed, 22 Apr 2020 05:45:01: 25000000 INFO @ Wed, 22 Apr 2020 05:45:04: 38000000 INFO @ Wed, 22 Apr 2020 05:45:05: 32000000 INFO @ Wed, 22 Apr 2020 05:45:05: 26000000 INFO @ Wed, 22 Apr 2020 05:45:09: 39000000 INFO @ Wed, 22 Apr 2020 05:45:10: 33000000 INFO @ Wed, 22 Apr 2020 05:45:10: 27000000 INFO @ Wed, 22 Apr 2020 05:45:14: 40000000 INFO @ Wed, 22 Apr 2020 05:45:15: 34000000 INFO @ Wed, 22 Apr 2020 05:45:15: 28000000 INFO @ Wed, 22 Apr 2020 05:45:19: 41000000 INFO @ Wed, 22 Apr 2020 05:45:20: 35000000 INFO @ Wed, 22 Apr 2020 05:45:20: 29000000 INFO @ Wed, 22 Apr 2020 05:45:24: 42000000 INFO @ Wed, 22 Apr 2020 05:45:25: 36000000 INFO @ Wed, 22 Apr 2020 05:45:25: 30000000 INFO @ Wed, 22 Apr 2020 05:45:29: 43000000 INFO @ Wed, 22 Apr 2020 05:45:30: 37000000 INFO @ Wed, 22 Apr 2020 05:45:30: 31000000 INFO @ Wed, 22 Apr 2020 05:45:34: 44000000 INFO @ Wed, 22 Apr 2020 05:45:35: 38000000 INFO @ Wed, 22 Apr 2020 05:45:35: 32000000 INFO @ Wed, 22 Apr 2020 05:45:39: 45000000 INFO @ Wed, 22 Apr 2020 05:45:39: 39000000 INFO @ Wed, 22 Apr 2020 05:45:40: 33000000 INFO @ Wed, 22 Apr 2020 05:45:44: 46000000 INFO @ Wed, 22 Apr 2020 05:45:44: 40000000 INFO @ Wed, 22 Apr 2020 05:45:45: 34000000 INFO @ Wed, 22 Apr 2020 05:45:49: 47000000 INFO @ Wed, 22 Apr 2020 05:45:49: 41000000 INFO @ Wed, 22 Apr 2020 05:45:50: 35000000 INFO @ Wed, 22 Apr 2020 05:45:54: 48000000 INFO @ Wed, 22 Apr 2020 05:45:54: 42000000 INFO @ Wed, 22 Apr 2020 05:45:55: 36000000 INFO @ Wed, 22 Apr 2020 05:45:59: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 05:45:59: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 05:45:59: #1 total tags in treatment: 48970911 INFO @ Wed, 22 Apr 2020 05:45:59: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:45:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 05:45:59: 43000000 INFO @ Wed, 22 Apr 2020 05:46:00: 37000000 INFO @ Wed, 22 Apr 2020 05:46:00: #1 tags after filtering in treatment: 48970734 INFO @ Wed, 22 Apr 2020 05:46:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:46:00: #1 finished! INFO @ Wed, 22 Apr 2020 05:46:00: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:46:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:46:04: 44000000 INFO @ Wed, 22 Apr 2020 05:46:05: 38000000 INFO @ Wed, 22 Apr 2020 05:46:09: #2 number of paired peaks: 111430 INFO @ Wed, 22 Apr 2020 05:46:09: start model_add_line... INFO @ Wed, 22 Apr 2020 05:46:09: 45000000 INFO @ Wed, 22 Apr 2020 05:46:10: 39000000 INFO @ Wed, 22 Apr 2020 05:46:10: start X-correlation... INFO @ Wed, 22 Apr 2020 05:46:10: end of X-cor INFO @ Wed, 22 Apr 2020 05:46:10: #2 finished! INFO @ Wed, 22 Apr 2020 05:46:10: #2 predicted fragment length is 130 bps INFO @ Wed, 22 Apr 2020 05:46:10: #2 alternative fragment length(s) may be 3,130 bps INFO @ Wed, 22 Apr 2020 05:46:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.05_model.r INFO @ Wed, 22 Apr 2020 05:46:10: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:46:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:46:14: 46000000 INFO @ Wed, 22 Apr 2020 05:46:15: 40000000 INFO @ Wed, 22 Apr 2020 05:46:19: 47000000 INFO @ Wed, 22 Apr 2020 05:46:20: 41000000 INFO @ Wed, 22 Apr 2020 05:46:25: 48000000 INFO @ Wed, 22 Apr 2020 05:46:25: 42000000 INFO @ Wed, 22 Apr 2020 05:46:30: 43000000 INFO @ Wed, 22 Apr 2020 05:46:30: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 05:46:30: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 05:46:30: #1 total tags in treatment: 48970911 INFO @ Wed, 22 Apr 2020 05:46:30: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:46:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 05:46:31: #1 tags after filtering in treatment: 48970734 INFO @ Wed, 22 Apr 2020 05:46:31: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:46:31: #1 finished! INFO @ Wed, 22 Apr 2020 05:46:31: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:46:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:46:34: 44000000 INFO @ Wed, 22 Apr 2020 05:46:39: 45000000 INFO @ Wed, 22 Apr 2020 05:46:39: #2 number of paired peaks: 111430 INFO @ Wed, 22 Apr 2020 05:46:39: start model_add_line... INFO @ Wed, 22 Apr 2020 05:46:40: start X-correlation... INFO @ Wed, 22 Apr 2020 05:46:40: end of X-cor INFO @ Wed, 22 Apr 2020 05:46:40: #2 finished! INFO @ Wed, 22 Apr 2020 05:46:40: #2 predicted fragment length is 130 bps INFO @ Wed, 22 Apr 2020 05:46:40: #2 alternative fragment length(s) may be 3,130 bps INFO @ Wed, 22 Apr 2020 05:46:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.10_model.r INFO @ Wed, 22 Apr 2020 05:46:40: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:46:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:46:44: 46000000 INFO @ Wed, 22 Apr 2020 05:46:49: 47000000 INFO @ Wed, 22 Apr 2020 05:46:54: 48000000 INFO @ Wed, 22 Apr 2020 05:46:59: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 05:46:59: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 05:46:59: #1 total tags in treatment: 48970911 INFO @ Wed, 22 Apr 2020 05:46:59: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:46:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 05:47:00: #1 tags after filtering in treatment: 48970734 INFO @ Wed, 22 Apr 2020 05:47:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:47:00: #1 finished! INFO @ Wed, 22 Apr 2020 05:47:00: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:47:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:47:09: #2 number of paired peaks: 111430 INFO @ Wed, 22 Apr 2020 05:47:09: start model_add_line... INFO @ Wed, 22 Apr 2020 05:47:10: start X-correlation... INFO @ Wed, 22 Apr 2020 05:47:10: end of X-cor INFO @ Wed, 22 Apr 2020 05:47:10: #2 finished! INFO @ Wed, 22 Apr 2020 05:47:10: #2 predicted fragment length is 130 bps INFO @ Wed, 22 Apr 2020 05:47:10: #2 alternative fragment length(s) may be 3,130 bps INFO @ Wed, 22 Apr 2020 05:47:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.20_model.r INFO @ Wed, 22 Apr 2020 05:47:10: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:47:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:47:59: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:48:30: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:48:58: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:49:03: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.05_peaks.xls INFO @ Wed, 22 Apr 2020 05:49:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:49:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.05_summits.bed INFO @ Wed, 22 Apr 2020 05:49:04: Done! pass1 - making usageList (193 chroms): 13 millis pass2 - checking and writing primary data (90771 records, 4 fields): 86 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:49:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.10_peaks.xls INFO @ Wed, 22 Apr 2020 05:49:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:49:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.10_summits.bed INFO @ Wed, 22 Apr 2020 05:49:33: Done! pass1 - making usageList (160 chroms): 9 millis pass2 - checking and writing primary data (68180 records, 4 fields): 63 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:50:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.20_peaks.xls INFO @ Wed, 22 Apr 2020 05:50:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:50:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101911/ERX101911.20_summits.bed INFO @ Wed, 22 Apr 2020 05:50:01: Done! pass1 - making usageList (136 chroms): 6 millis pass2 - checking and writing primary data (46408 records, 4 fields): 46 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。