Job ID = 14160629 SRX = SRX8582570 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 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: 00:26:01 31357554 reads; of these: 31357554 (100.00%) were paired; of these: 2928824 (9.34%) aligned concordantly 0 times 23920600 (76.28%) aligned concordantly exactly 1 time 4508130 (14.38%) aligned concordantly >1 times ---- 2928824 pairs aligned concordantly 0 times; of these: 1502707 (51.31%) aligned discordantly 1 time ---- 1426117 pairs aligned 0 times concordantly or discordantly; of these: 2852234 mates make up the pairs; of these: 1593637 (55.87%) aligned 0 times 693119 (24.30%) aligned exactly 1 time 565478 (19.83%) aligned >1 times 97.46% overall alignment rate Time searching: 00:26:01 Overall time: 00:26:01 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 28 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 8879958 / 29917222 = 0.2968 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 04:04:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 09 Dec 2021 04:04:23: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:04:23: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:04:27: 1000000 INFO @ Thu, 09 Dec 2021 04:04:32: 2000000 INFO @ Thu, 09 Dec 2021 04:04:36: 3000000 INFO @ Thu, 09 Dec 2021 04:04:40: 4000000 INFO @ Thu, 09 Dec 2021 04:04:44: 5000000 INFO @ Thu, 09 Dec 2021 04:04:49: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 04:04:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 09 Dec 2021 04:04:53: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:04:53: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:04:53: 7000000 INFO @ Thu, 09 Dec 2021 04:04:58: 8000000 INFO @ Thu, 09 Dec 2021 04:04:58: 1000000 INFO @ Thu, 09 Dec 2021 04:05:02: 9000000 INFO @ Thu, 09 Dec 2021 04:05:03: 2000000 INFO @ Thu, 09 Dec 2021 04:05:07: 10000000 INFO @ Thu, 09 Dec 2021 04:05:08: 3000000 INFO @ Thu, 09 Dec 2021 04:05:12: 11000000 INFO @ Thu, 09 Dec 2021 04:05:13: 4000000 INFO @ Thu, 09 Dec 2021 04:05:16: 12000000 INFO @ Thu, 09 Dec 2021 04:05:17: 5000000 INFO @ Thu, 09 Dec 2021 04:05:21: 13000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 04:05:22: 6000000 INFO @ Thu, 09 Dec 2021 04:05:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 09 Dec 2021 04:05:23: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:05:23: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:05:26: 14000000 INFO @ Thu, 09 Dec 2021 04:05:27: 7000000 INFO @ Thu, 09 Dec 2021 04:05:28: 1000000 INFO @ Thu, 09 Dec 2021 04:05:30: 15000000 INFO @ Thu, 09 Dec 2021 04:05:31: 8000000 INFO @ Thu, 09 Dec 2021 04:05:34: 2000000 INFO @ Thu, 09 Dec 2021 04:05:35: 16000000 INFO @ Thu, 09 Dec 2021 04:05:36: 9000000 INFO @ Thu, 09 Dec 2021 04:05:40: 3000000 INFO @ Thu, 09 Dec 2021 04:05:40: 17000000 INFO @ Thu, 09 Dec 2021 04:05:41: 10000000 INFO @ Thu, 09 Dec 2021 04:05:45: 18000000 INFO @ Thu, 09 Dec 2021 04:05:45: 4000000 INFO @ Thu, 09 Dec 2021 04:05:46: 11000000 INFO @ Thu, 09 Dec 2021 04:05:49: 19000000 INFO @ Thu, 09 Dec 2021 04:05:50: 12000000 INFO @ Thu, 09 Dec 2021 04:05:51: 5000000 INFO @ Thu, 09 Dec 2021 04:05:54: 20000000 INFO @ Thu, 09 Dec 2021 04:05:55: 13000000 INFO @ Thu, 09 Dec 2021 04:05:57: 6000000 INFO @ Thu, 09 Dec 2021 04:05:59: 21000000 INFO @ Thu, 09 Dec 2021 04:06:00: 14000000 INFO @ Thu, 09 Dec 2021 04:06:02: 7000000 INFO @ Thu, 09 Dec 2021 04:06:04: 22000000 INFO @ Thu, 09 Dec 2021 04:06:05: 15000000 INFO @ Thu, 09 Dec 2021 04:06:08: 8000000 INFO @ Thu, 09 Dec 2021 04:06:09: 23000000 INFO @ Thu, 09 Dec 2021 04:06:09: 16000000 INFO @ Thu, 09 Dec 2021 04:06:13: 24000000 INFO @ Thu, 09 Dec 2021 04:06:13: 9000000 INFO @ Thu, 09 Dec 2021 04:06:14: 17000000 INFO @ Thu, 09 Dec 2021 04:06:18: 25000000 INFO @ Thu, 09 Dec 2021 04:06:19: 18000000 INFO @ Thu, 09 Dec 2021 04:06:19: 10000000 INFO @ Thu, 09 Dec 2021 04:06:23: 26000000 INFO @ Thu, 09 Dec 2021 04:06:24: 19000000 INFO @ Thu, 09 Dec 2021 04:06:25: 11000000 INFO @ Thu, 09 Dec 2021 04:06:28: 27000000 INFO @ Thu, 09 Dec 2021 04:06:29: 20000000 INFO @ Thu, 09 Dec 2021 04:06:30: 12000000 INFO @ Thu, 09 Dec 2021 04:06:32: 28000000 INFO @ Thu, 09 Dec 2021 04:06:34: 21000000 INFO @ Thu, 09 Dec 2021 04:06:36: 13000000 INFO @ Thu, 09 Dec 2021 04:06:37: 29000000 INFO @ Thu, 09 Dec 2021 04:06:38: 22000000 INFO @ Thu, 09 Dec 2021 04:06:42: 14000000 INFO @ Thu, 09 Dec 2021 04:06:42: 30000000 INFO @ Thu, 09 Dec 2021 04:06:43: 23000000 INFO @ Thu, 09 Dec 2021 04:06:47: 31000000 INFO @ Thu, 09 Dec 2021 04:06:47: 15000000 INFO @ Thu, 09 Dec 2021 04:06:48: 24000000 INFO @ Thu, 09 Dec 2021 04:06:52: 32000000 INFO @ Thu, 09 Dec 2021 04:06:53: 16000000 INFO @ Thu, 09 Dec 2021 04:06:53: 25000000 INFO @ Thu, 09 Dec 2021 04:06:56: 33000000 INFO @ Thu, 09 Dec 2021 04:06:58: 26000000 INFO @ Thu, 09 Dec 2021 04:06:58: 17000000 INFO @ Thu, 09 Dec 2021 04:07:01: 34000000 INFO @ Thu, 09 Dec 2021 04:07:03: 27000000 INFO @ Thu, 09 Dec 2021 04:07:04: 18000000 INFO @ Thu, 09 Dec 2021 04:07:06: 35000000 INFO @ Thu, 09 Dec 2021 04:07:07: 28000000 INFO @ Thu, 09 Dec 2021 04:07:10: 19000000 INFO @ Thu, 09 Dec 2021 04:07:11: 36000000 INFO @ Thu, 09 Dec 2021 04:07:12: 29000000 INFO @ Thu, 09 Dec 2021 04:07:15: 20000000 INFO @ Thu, 09 Dec 2021 04:07:15: 37000000 INFO @ Thu, 09 Dec 2021 04:07:17: 30000000 INFO @ Thu, 09 Dec 2021 04:07:20: 38000000 INFO @ Thu, 09 Dec 2021 04:07:21: 21000000 INFO @ Thu, 09 Dec 2021 04:07:22: 31000000 INFO @ Thu, 09 Dec 2021 04:07:25: 39000000 INFO @ Thu, 09 Dec 2021 04:07:26: 32000000 INFO @ Thu, 09 Dec 2021 04:07:27: 22000000 INFO @ Thu, 09 Dec 2021 04:07:30: 40000000 INFO @ Thu, 09 Dec 2021 04:07:31: 33000000 INFO @ Thu, 09 Dec 2021 04:07:32: 23000000 INFO @ Thu, 09 Dec 2021 04:07:35: 41000000 INFO @ Thu, 09 Dec 2021 04:07:36: 34000000 INFO @ Thu, 09 Dec 2021 04:07:38: 24000000 INFO @ Thu, 09 Dec 2021 04:07:39: 42000000 INFO @ Thu, 09 Dec 2021 04:07:41: 35000000 INFO @ Thu, 09 Dec 2021 04:07:44: 25000000 INFO @ Thu, 09 Dec 2021 04:07:44: 43000000 INFO @ Thu, 09 Dec 2021 04:07:46: 36000000 INFO @ Thu, 09 Dec 2021 04:07:46: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 04:07:46: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 04:07:46: #1 total tags in treatment: 19839764 INFO @ Thu, 09 Dec 2021 04:07:46: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:07:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:07:46: #1 tags after filtering in treatment: 17163911 INFO @ Thu, 09 Dec 2021 04:07:46: #1 Redundant rate of treatment: 0.13 INFO @ Thu, 09 Dec 2021 04:07:46: #1 finished! INFO @ Thu, 09 Dec 2021 04:07:46: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:07:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:07:47: #2 number of paired peaks: 405 WARNING @ Thu, 09 Dec 2021 04:07:47: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Thu, 09 Dec 2021 04:07:47: start model_add_line... INFO @ Thu, 09 Dec 2021 04:07:47: start X-correlation... INFO @ Thu, 09 Dec 2021 04:07:47: end of X-cor INFO @ Thu, 09 Dec 2021 04:07:47: #2 finished! INFO @ Thu, 09 Dec 2021 04:07:47: #2 predicted fragment length is 136 bps INFO @ Thu, 09 Dec 2021 04:07:47: #2 alternative fragment length(s) may be 4,136 bps INFO @ Thu, 09 Dec 2021 04:07:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.05_model.r INFO @ Thu, 09 Dec 2021 04:07:47: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:07:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:07:49: 26000000 INFO @ Thu, 09 Dec 2021 04:07:50: 37000000 INFO @ Thu, 09 Dec 2021 04:07:55: 27000000 INFO @ Thu, 09 Dec 2021 04:07:55: 38000000 INFO @ Thu, 09 Dec 2021 04:08:00: 39000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:08:00: 28000000 INFO @ Thu, 09 Dec 2021 04:08:04: 40000000 INFO @ Thu, 09 Dec 2021 04:08:06: 29000000 INFO @ Thu, 09 Dec 2021 04:08:09: 41000000 INFO @ Thu, 09 Dec 2021 04:08:12: 30000000 INFO @ Thu, 09 Dec 2021 04:08:14: 42000000 INFO @ Thu, 09 Dec 2021 04:08:17: 31000000 INFO @ Thu, 09 Dec 2021 04:08:18: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:08:19: 43000000 INFO @ Thu, 09 Dec 2021 04:08:20: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 04:08:20: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 04:08:20: #1 total tags in treatment: 19839764 INFO @ Thu, 09 Dec 2021 04:08:20: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:08:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:08:21: #1 tags after filtering in treatment: 17163911 INFO @ Thu, 09 Dec 2021 04:08:21: #1 Redundant rate of treatment: 0.13 INFO @ Thu, 09 Dec 2021 04:08:21: #1 finished! INFO @ Thu, 09 Dec 2021 04:08:21: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:08:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:08:22: #2 number of paired peaks: 405 WARNING @ Thu, 09 Dec 2021 04:08:22: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Thu, 09 Dec 2021 04:08:22: start model_add_line... INFO @ Thu, 09 Dec 2021 04:08:22: start X-correlation... INFO @ Thu, 09 Dec 2021 04:08:22: end of X-cor INFO @ Thu, 09 Dec 2021 04:08:22: #2 finished! INFO @ Thu, 09 Dec 2021 04:08:22: #2 predicted fragment length is 136 bps INFO @ Thu, 09 Dec 2021 04:08:22: #2 alternative fragment length(s) may be 4,136 bps INFO @ Thu, 09 Dec 2021 04:08:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.10_model.r INFO @ Thu, 09 Dec 2021 04:08:22: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:08:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:08:23: 32000000 INFO @ Thu, 09 Dec 2021 04:08:28: 33000000 INFO @ Thu, 09 Dec 2021 04:08:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:08:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:08:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.05_summits.bed INFO @ Thu, 09 Dec 2021 04:08:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5038 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:08:33: 34000000 INFO @ Thu, 09 Dec 2021 04:08:39: 35000000 INFO @ Thu, 09 Dec 2021 04:08:44: 36000000 INFO @ Thu, 09 Dec 2021 04:08:50: 37000000 INFO @ Thu, 09 Dec 2021 04:08:54: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:08:55: 38000000 INFO @ Thu, 09 Dec 2021 04:09:00: 39000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:09:05: 40000000 INFO @ Thu, 09 Dec 2021 04:09:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:09:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:09:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.10_summits.bed INFO @ Thu, 09 Dec 2021 04:09:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2802 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:09:11: 41000000 INFO @ Thu, 09 Dec 2021 04:09:16: 42000000 INFO @ Thu, 09 Dec 2021 04:09:22: 43000000 INFO @ Thu, 09 Dec 2021 04:09:24: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 04:09:24: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 04:09:24: #1 total tags in treatment: 19839764 INFO @ Thu, 09 Dec 2021 04:09:24: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:09:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:09:24: #1 tags after filtering in treatment: 17163911 INFO @ Thu, 09 Dec 2021 04:09:24: #1 Redundant rate of treatment: 0.13 INFO @ Thu, 09 Dec 2021 04:09:24: #1 finished! INFO @ Thu, 09 Dec 2021 04:09:24: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:09:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:09:25: #2 number of paired peaks: 405 WARNING @ Thu, 09 Dec 2021 04:09:25: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Thu, 09 Dec 2021 04:09:25: start model_add_line... INFO @ Thu, 09 Dec 2021 04:09:25: start X-correlation... INFO @ Thu, 09 Dec 2021 04:09:25: end of X-cor INFO @ Thu, 09 Dec 2021 04:09:25: #2 finished! INFO @ Thu, 09 Dec 2021 04:09:25: #2 predicted fragment length is 136 bps INFO @ Thu, 09 Dec 2021 04:09:25: #2 alternative fragment length(s) may be 4,136 bps INFO @ Thu, 09 Dec 2021 04:09:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.20_model.r INFO @ Thu, 09 Dec 2021 04:09:25: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:09:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:09:57: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:10:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:10:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:10:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8582570/SRX8582570.20_summits.bed INFO @ Thu, 09 Dec 2021 04:10:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1170 records, 4 fields): 3 millis CompletedMACS2peakCalling