Job ID = 14159291 SRX = SRX8976720 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: 00:00:01 Multiseed full-index search: 00:11:39 12492052 reads; of these: 12492052 (100.00%) were paired; of these: 896590 (7.18%) aligned concordantly 0 times 9653221 (77.27%) aligned concordantly exactly 1 time 1942241 (15.55%) aligned concordantly >1 times ---- 896590 pairs aligned concordantly 0 times; of these: 511431 (57.04%) aligned discordantly 1 time ---- 385159 pairs aligned 0 times concordantly or discordantly; of these: 770318 mates make up the pairs; of these: 459693 (59.68%) aligned 0 times 128001 (16.62%) aligned exactly 1 time 182624 (23.71%) aligned >1 times 98.16% overall alignment rate Time searching: 00:11:40 Overall time: 00:11:40 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 12 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] 5465183 / 12102418 = 0.4516 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 @ Wed, 08 Dec 2021 20:58:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.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 @ Wed, 08 Dec 2021 20:58:41: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:58:41: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:58:47: 1000000 INFO @ Wed, 08 Dec 2021 20:58:52: 2000000 INFO @ Wed, 08 Dec 2021 20:58:57: 3000000 INFO @ Wed, 08 Dec 2021 20:59:01: 4000000 INFO @ Wed, 08 Dec 2021 20:59:06: 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 @ Wed, 08 Dec 2021 20:59:11: 6000000 INFO @ Wed, 08 Dec 2021 20:59:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.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 @ Wed, 08 Dec 2021 20:59:11: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:59:11: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:59:16: 7000000 INFO @ Wed, 08 Dec 2021 20:59:17: 1000000 INFO @ Wed, 08 Dec 2021 20:59:21: 8000000 INFO @ Wed, 08 Dec 2021 20:59:22: 2000000 INFO @ Wed, 08 Dec 2021 20:59:26: 9000000 INFO @ Wed, 08 Dec 2021 20:59:28: 3000000 INFO @ Wed, 08 Dec 2021 20:59:32: 10000000 INFO @ Wed, 08 Dec 2021 20:59:33: 4000000 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 @ Wed, 08 Dec 2021 20:59:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.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 @ Wed, 08 Dec 2021 20:59:37: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:59:37: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:59:38: 11000000 INFO @ Wed, 08 Dec 2021 20:59:39: 5000000 INFO @ Wed, 08 Dec 2021 20:59:43: 1000000 INFO @ Wed, 08 Dec 2021 20:59:44: 12000000 INFO @ Wed, 08 Dec 2021 20:59:44: 6000000 INFO @ Wed, 08 Dec 2021 20:59:49: 13000000 INFO @ Wed, 08 Dec 2021 20:59:50: 7000000 INFO @ Wed, 08 Dec 2021 20:59:50: 2000000 INFO @ Wed, 08 Dec 2021 20:59:53: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:59:53: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:59:53: #1 total tags in treatment: 6299283 INFO @ Wed, 08 Dec 2021 20:59:53: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:59:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 20:59:53: #1 tags after filtering in treatment: 5885330 INFO @ Wed, 08 Dec 2021 20:59:53: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 20:59:53: #1 finished! INFO @ Wed, 08 Dec 2021 20:59:53: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:59:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:59:53: #2 number of paired peaks: 767 WARNING @ Wed, 08 Dec 2021 20:59:53: Fewer paired peaks (767) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 767 pairs to build model! INFO @ Wed, 08 Dec 2021 20:59:53: start model_add_line... INFO @ Wed, 08 Dec 2021 20:59:53: start X-correlation... INFO @ Wed, 08 Dec 2021 20:59:53: end of X-cor INFO @ Wed, 08 Dec 2021 20:59:53: #2 finished! INFO @ Wed, 08 Dec 2021 20:59:53: #2 predicted fragment length is 160 bps INFO @ Wed, 08 Dec 2021 20:59:53: #2 alternative fragment length(s) may be 4,160 bps INFO @ Wed, 08 Dec 2021 20:59:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.05_model.r INFO @ Wed, 08 Dec 2021 20:59:53: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:59:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:59:56: 8000000 INFO @ Wed, 08 Dec 2021 20:59:56: 3000000 INFO @ Wed, 08 Dec 2021 21:00:01: 9000000 INFO @ Wed, 08 Dec 2021 21:00:02: 4000000 INFO @ Wed, 08 Dec 2021 21:00:07: 10000000 INFO @ Wed, 08 Dec 2021 21:00:07: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:00:09: 5000000 INFO @ Wed, 08 Dec 2021 21:00:13: 11000000 INFO @ Wed, 08 Dec 2021 21:00:15: 6000000 INFO @ Wed, 08 Dec 2021 21:00:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:00:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:00:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.05_summits.bed INFO @ Wed, 08 Dec 2021 21:00:16: Done! INFO @ Wed, 08 Dec 2021 21:00:19: 12000000 INFO @ Wed, 08 Dec 2021 21:00:20: 7000000 INFO @ Wed, 08 Dec 2021 21:00:24: 13000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (551 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:00:26: 8000000 INFO @ Wed, 08 Dec 2021 21:00:28: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 21:00:28: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 21:00:28: #1 total tags in treatment: 6299283 INFO @ Wed, 08 Dec 2021 21:00:28: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:00:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 21:00:28: #1 tags after filtering in treatment: 5885330 INFO @ Wed, 08 Dec 2021 21:00:28: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 21:00:28: #1 finished! INFO @ Wed, 08 Dec 2021 21:00:28: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:00:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:00:28: #2 number of paired peaks: 767 WARNING @ Wed, 08 Dec 2021 21:00:28: Fewer paired peaks (767) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 767 pairs to build model! INFO @ Wed, 08 Dec 2021 21:00:28: start model_add_line... INFO @ Wed, 08 Dec 2021 21:00:28: start X-correlation... INFO @ Wed, 08 Dec 2021 21:00:28: end of X-cor INFO @ Wed, 08 Dec 2021 21:00:28: #2 finished! INFO @ Wed, 08 Dec 2021 21:00:28: #2 predicted fragment length is 160 bps INFO @ Wed, 08 Dec 2021 21:00:28: #2 alternative fragment length(s) may be 4,160 bps INFO @ Wed, 08 Dec 2021 21:00:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.10_model.r INFO @ Wed, 08 Dec 2021 21:00:28: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:00:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:00:32: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:00:37: 10000000 INFO @ Wed, 08 Dec 2021 21:00:43: 11000000 INFO @ Wed, 08 Dec 2021 21:00:45: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:00:51: 12000000 INFO @ Wed, 08 Dec 2021 21:00:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:00:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:00:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.10_summits.bed INFO @ Wed, 08 Dec 2021 21:00:54: Done! INFO @ Wed, 08 Dec 2021 21:00:57: 13000000 pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (332 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:01:00: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 21:01:00: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 21:01:00: #1 total tags in treatment: 6299283 INFO @ Wed, 08 Dec 2021 21:01:00: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:01:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 21:01:00: #1 tags after filtering in treatment: 5885330 INFO @ Wed, 08 Dec 2021 21:01:00: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 21:01:00: #1 finished! INFO @ Wed, 08 Dec 2021 21:01:00: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:01:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:01:01: #2 number of paired peaks: 767 WARNING @ Wed, 08 Dec 2021 21:01:01: Fewer paired peaks (767) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 767 pairs to build model! INFO @ Wed, 08 Dec 2021 21:01:01: start model_add_line... INFO @ Wed, 08 Dec 2021 21:01:01: start X-correlation... INFO @ Wed, 08 Dec 2021 21:01:01: end of X-cor INFO @ Wed, 08 Dec 2021 21:01:01: #2 finished! INFO @ Wed, 08 Dec 2021 21:01:01: #2 predicted fragment length is 160 bps INFO @ Wed, 08 Dec 2021 21:01:01: #2 alternative fragment length(s) may be 4,160 bps INFO @ Wed, 08 Dec 2021 21:01:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.20_model.r INFO @ Wed, 08 Dec 2021 21:01:01: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:01:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:01:15: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:01:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:01:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:01:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976720/SRX8976720.20_summits.bed INFO @ Wed, 08 Dec 2021 21:01:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (209 records, 4 fields): 1 millis CompletedMACS2peakCalling