Job ID = 14160631 SRX = SRX8582580 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: 00:21:29 26824028 reads; of these: 26824028 (100.00%) were paired; of these: 4213033 (15.71%) aligned concordantly 0 times 19147548 (71.38%) aligned concordantly exactly 1 time 3463447 (12.91%) aligned concordantly >1 times ---- 4213033 pairs aligned concordantly 0 times; of these: 1835298 (43.56%) aligned discordantly 1 time ---- 2377735 pairs aligned 0 times concordantly or discordantly; of these: 4755470 mates make up the pairs; of these: 3243322 (68.20%) aligned 0 times 939290 (19.75%) aligned exactly 1 time 572858 (12.05%) aligned >1 times 93.95% overall alignment rate Time searching: 00:21:29 Overall time: 00:21:29 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 24 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] 6745938 / 24434911 = 0.2761 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 03:58:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.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 03:58:36: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:58:36: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:58:42: 1000000 INFO @ Thu, 09 Dec 2021 03:58:47: 2000000 INFO @ Thu, 09 Dec 2021 03:58:53: 3000000 INFO @ Thu, 09 Dec 2021 03:58:58: 4000000 INFO @ Thu, 09 Dec 2021 03:59:03: 5000000 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 03:59:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.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 03:59:06: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:59:06: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:59:08: 6000000 INFO @ Thu, 09 Dec 2021 03:59:12: 1000000 INFO @ Thu, 09 Dec 2021 03:59:14: 7000000 INFO @ Thu, 09 Dec 2021 03:59:18: 2000000 INFO @ Thu, 09 Dec 2021 03:59:19: 8000000 INFO @ Thu, 09 Dec 2021 03:59:23: 3000000 INFO @ Thu, 09 Dec 2021 03:59:24: 9000000 INFO @ Thu, 09 Dec 2021 03:59:28: 4000000 INFO @ Thu, 09 Dec 2021 03:59:29: 10000000 INFO @ Thu, 09 Dec 2021 03:59:33: 5000000 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 03:59:34: 11000000 INFO @ Thu, 09 Dec 2021 03:59:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.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 03:59:36: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:59:36: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:59:39: 6000000 INFO @ Thu, 09 Dec 2021 03:59:40: 12000000 INFO @ Thu, 09 Dec 2021 03:59:42: 1000000 INFO @ Thu, 09 Dec 2021 03:59:44: 7000000 INFO @ Thu, 09 Dec 2021 03:59:46: 13000000 INFO @ Thu, 09 Dec 2021 03:59:47: 2000000 INFO @ Thu, 09 Dec 2021 03:59:50: 8000000 INFO @ Thu, 09 Dec 2021 03:59:52: 14000000 INFO @ Thu, 09 Dec 2021 03:59:53: 3000000 INFO @ Thu, 09 Dec 2021 03:59:56: 9000000 INFO @ Thu, 09 Dec 2021 03:59:57: 15000000 INFO @ Thu, 09 Dec 2021 03:59:59: 4000000 INFO @ Thu, 09 Dec 2021 04:00:02: 10000000 INFO @ Thu, 09 Dec 2021 04:00:03: 16000000 INFO @ Thu, 09 Dec 2021 04:00:04: 5000000 INFO @ Thu, 09 Dec 2021 04:00:08: 11000000 INFO @ Thu, 09 Dec 2021 04:00:09: 17000000 INFO @ Thu, 09 Dec 2021 04:00:10: 6000000 INFO @ Thu, 09 Dec 2021 04:00:13: 12000000 INFO @ Thu, 09 Dec 2021 04:00:14: 18000000 INFO @ Thu, 09 Dec 2021 04:00:15: 7000000 INFO @ Thu, 09 Dec 2021 04:00:19: 13000000 INFO @ Thu, 09 Dec 2021 04:00:20: 19000000 INFO @ Thu, 09 Dec 2021 04:00:21: 8000000 INFO @ Thu, 09 Dec 2021 04:00:25: 14000000 INFO @ Thu, 09 Dec 2021 04:00:26: 20000000 INFO @ Thu, 09 Dec 2021 04:00:27: 9000000 INFO @ Thu, 09 Dec 2021 04:00:31: 15000000 INFO @ Thu, 09 Dec 2021 04:00:31: 21000000 INFO @ Thu, 09 Dec 2021 04:00:32: 10000000 INFO @ Thu, 09 Dec 2021 04:00:36: 16000000 INFO @ Thu, 09 Dec 2021 04:00:37: 22000000 INFO @ Thu, 09 Dec 2021 04:00:38: 11000000 INFO @ Thu, 09 Dec 2021 04:00:42: 17000000 INFO @ Thu, 09 Dec 2021 04:00:43: 23000000 INFO @ Thu, 09 Dec 2021 04:00:43: 12000000 INFO @ Thu, 09 Dec 2021 04:00:48: 18000000 INFO @ Thu, 09 Dec 2021 04:00:48: 24000000 INFO @ Thu, 09 Dec 2021 04:00:49: 13000000 INFO @ Thu, 09 Dec 2021 04:00:54: 19000000 INFO @ Thu, 09 Dec 2021 04:00:54: 25000000 INFO @ Thu, 09 Dec 2021 04:00:55: 14000000 INFO @ Thu, 09 Dec 2021 04:00:59: 20000000 INFO @ Thu, 09 Dec 2021 04:00:59: 26000000 INFO @ Thu, 09 Dec 2021 04:01:00: 15000000 INFO @ Thu, 09 Dec 2021 04:01:05: 21000000 INFO @ Thu, 09 Dec 2021 04:01:05: 27000000 INFO @ Thu, 09 Dec 2021 04:01:06: 16000000 INFO @ Thu, 09 Dec 2021 04:01:11: 22000000 INFO @ Thu, 09 Dec 2021 04:01:11: 28000000 INFO @ Thu, 09 Dec 2021 04:01:11: 17000000 INFO @ Thu, 09 Dec 2021 04:01:16: 23000000 INFO @ Thu, 09 Dec 2021 04:01:17: 29000000 INFO @ Thu, 09 Dec 2021 04:01:17: 18000000 INFO @ Thu, 09 Dec 2021 04:01:22: 24000000 INFO @ Thu, 09 Dec 2021 04:01:22: 30000000 INFO @ Thu, 09 Dec 2021 04:01:23: 19000000 INFO @ Thu, 09 Dec 2021 04:01:28: 25000000 INFO @ Thu, 09 Dec 2021 04:01:28: 31000000 INFO @ Thu, 09 Dec 2021 04:01:28: 20000000 INFO @ Thu, 09 Dec 2021 04:01:33: 26000000 INFO @ Thu, 09 Dec 2021 04:01:34: 32000000 INFO @ Thu, 09 Dec 2021 04:01:34: 21000000 INFO @ Thu, 09 Dec 2021 04:01:39: 27000000 INFO @ Thu, 09 Dec 2021 04:01:39: 33000000 INFO @ Thu, 09 Dec 2021 04:01:39: 22000000 INFO @ Thu, 09 Dec 2021 04:01:45: 28000000 INFO @ Thu, 09 Dec 2021 04:01:45: 34000000 INFO @ Thu, 09 Dec 2021 04:01:45: 23000000 INFO @ Thu, 09 Dec 2021 04:01:50: 29000000 INFO @ Thu, 09 Dec 2021 04:01:51: 35000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:01:51: 24000000 INFO @ Thu, 09 Dec 2021 04:01:56: 30000000 INFO @ Thu, 09 Dec 2021 04:01:56: 36000000 INFO @ Thu, 09 Dec 2021 04:01:56: 25000000 INFO @ Thu, 09 Dec 2021 04:02:01: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 04:02:01: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 04:02:01: #1 total tags in treatment: 16185018 INFO @ Thu, 09 Dec 2021 04:02:01: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:02:01: #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 04:02:02: 31000000 INFO @ Thu, 09 Dec 2021 04:02:02: #1 tags after filtering in treatment: 14448841 INFO @ Thu, 09 Dec 2021 04:02:02: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 09 Dec 2021 04:02:02: #1 finished! INFO @ Thu, 09 Dec 2021 04:02:02: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:02:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:02:02: 26000000 INFO @ Thu, 09 Dec 2021 04:02:03: #2 number of paired peaks: 399 WARNING @ Thu, 09 Dec 2021 04:02:03: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Thu, 09 Dec 2021 04:02:03: start model_add_line... INFO @ Thu, 09 Dec 2021 04:02:03: start X-correlation... INFO @ Thu, 09 Dec 2021 04:02:03: end of X-cor INFO @ Thu, 09 Dec 2021 04:02:03: #2 finished! INFO @ Thu, 09 Dec 2021 04:02:03: #2 predicted fragment length is 136 bps INFO @ Thu, 09 Dec 2021 04:02:03: #2 alternative fragment length(s) may be 4,125,132,136 bps INFO @ Thu, 09 Dec 2021 04:02:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.05_model.r INFO @ Thu, 09 Dec 2021 04:02:03: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:02:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:02:07: 32000000 INFO @ Thu, 09 Dec 2021 04:02:07: 27000000 INFO @ Thu, 09 Dec 2021 04:02:13: 33000000 INFO @ Thu, 09 Dec 2021 04:02:13: 28000000 INFO @ Thu, 09 Dec 2021 04:02:19: 29000000 INFO @ Thu, 09 Dec 2021 04:02:19: 34000000 INFO @ Thu, 09 Dec 2021 04:02:24: 30000000 INFO @ Thu, 09 Dec 2021 04:02:24: 35000000 INFO @ Thu, 09 Dec 2021 04:02:30: 31000000 INFO @ Thu, 09 Dec 2021 04:02:30: 36000000 INFO @ Thu, 09 Dec 2021 04:02:30: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:02:35: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 04:02:35: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 04:02:35: #1 total tags in treatment: 16185018 INFO @ Thu, 09 Dec 2021 04:02:35: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:02:35: #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 04:02:35: 32000000 INFO @ Thu, 09 Dec 2021 04:02:35: #1 tags after filtering in treatment: 14448841 INFO @ Thu, 09 Dec 2021 04:02:35: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 09 Dec 2021 04:02:35: #1 finished! INFO @ Thu, 09 Dec 2021 04:02:35: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:02:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:02:36: #2 number of paired peaks: 399 WARNING @ Thu, 09 Dec 2021 04:02:36: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Thu, 09 Dec 2021 04:02:36: start model_add_line... INFO @ Thu, 09 Dec 2021 04:02:36: start X-correlation... INFO @ Thu, 09 Dec 2021 04:02:36: end of X-cor INFO @ Thu, 09 Dec 2021 04:02:36: #2 finished! INFO @ Thu, 09 Dec 2021 04:02:36: #2 predicted fragment length is 136 bps INFO @ Thu, 09 Dec 2021 04:02:36: #2 alternative fragment length(s) may be 4,125,132,136 bps INFO @ Thu, 09 Dec 2021 04:02:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.10_model.r INFO @ Thu, 09 Dec 2021 04:02:36: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:02:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:02:41: 33000000 INFO @ Thu, 09 Dec 2021 04:02:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:02:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:02:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.05_summits.bed INFO @ Thu, 09 Dec 2021 04:02:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3866 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:02:46: 34000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:02:51: 35000000 INFO @ Thu, 09 Dec 2021 04:02:56: 36000000 INFO @ Thu, 09 Dec 2021 04:03:01: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 04:03:01: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 04:03:01: #1 total tags in treatment: 16185018 INFO @ Thu, 09 Dec 2021 04:03:01: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:03:01: #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 04:03:01: #1 tags after filtering in treatment: 14448841 INFO @ Thu, 09 Dec 2021 04:03:01: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 09 Dec 2021 04:03:01: #1 finished! INFO @ Thu, 09 Dec 2021 04:03:01: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:03:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:03:02: #2 number of paired peaks: 399 WARNING @ Thu, 09 Dec 2021 04:03:02: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Thu, 09 Dec 2021 04:03:02: start model_add_line... INFO @ Thu, 09 Dec 2021 04:03:02: start X-correlation... INFO @ Thu, 09 Dec 2021 04:03:02: end of X-cor INFO @ Thu, 09 Dec 2021 04:03:02: #2 finished! INFO @ Thu, 09 Dec 2021 04:03:02: #2 predicted fragment length is 136 bps INFO @ Thu, 09 Dec 2021 04:03:02: #2 alternative fragment length(s) may be 4,125,132,136 bps INFO @ Thu, 09 Dec 2021 04:03:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.20_model.r INFO @ Thu, 09 Dec 2021 04:03:02: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:03:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:03:03: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:03:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:03:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:03:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.10_summits.bed INFO @ Thu, 09 Dec 2021 04:03:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1962 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:03:29: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:03:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:03:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:03:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8582580/SRX8582580.20_summits.bed INFO @ Thu, 09 Dec 2021 04:03:43: Done! pass1 - making usageList (7 chroms): 37 millis pass2 - checking and writing primary data (787 records, 4 fields): 56 millis CompletedMACS2peakCalling