Job ID = 14159315 SRX = SRX8976729 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: 00:09:08 12407286 reads; of these: 12407286 (100.00%) were paired; of these: 855321 (6.89%) aligned concordantly 0 times 10060500 (81.09%) aligned concordantly exactly 1 time 1491465 (12.02%) aligned concordantly >1 times ---- 855321 pairs aligned concordantly 0 times; of these: 632748 (73.98%) aligned discordantly 1 time ---- 222573 pairs aligned 0 times concordantly or discordantly; of these: 445146 mates make up the pairs; of these: 125247 (28.14%) aligned 0 times 143004 (32.13%) aligned exactly 1 time 176895 (39.74%) aligned >1 times 99.50% overall alignment rate Time searching: 00:09:08 Overall time: 00:09:08 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 8 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] 323314 / 12154445 = 0.0266 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 21:08:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.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 21:08:16: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:08:16: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:08:22: 1000000 INFO @ Wed, 08 Dec 2021 21:08:28: 2000000 INFO @ Wed, 08 Dec 2021 21:08:34: 3000000 INFO @ Wed, 08 Dec 2021 21:08:40: 4000000 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 21:08:46: 5000000 INFO @ Wed, 08 Dec 2021 21:08:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.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 21:08:46: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:08:46: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:08:52: 6000000 INFO @ Wed, 08 Dec 2021 21:08:52: 1000000 INFO @ Wed, 08 Dec 2021 21:08:58: 2000000 INFO @ Wed, 08 Dec 2021 21:08:59: 7000000 INFO @ Wed, 08 Dec 2021 21:09:04: 3000000 INFO @ Wed, 08 Dec 2021 21:09:05: 8000000 INFO @ Wed, 08 Dec 2021 21:09:10: 4000000 INFO @ Wed, 08 Dec 2021 21:09:12: 9000000 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 21:09:16: 5000000 INFO @ Wed, 08 Dec 2021 21:09:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.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 21:09:16: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:09:16: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:09:18: 10000000 INFO @ Wed, 08 Dec 2021 21:09:22: 6000000 INFO @ Wed, 08 Dec 2021 21:09:23: 1000000 INFO @ Wed, 08 Dec 2021 21:09:25: 11000000 INFO @ Wed, 08 Dec 2021 21:09:28: 7000000 INFO @ Wed, 08 Dec 2021 21:09:29: 2000000 INFO @ Wed, 08 Dec 2021 21:09:31: 12000000 INFO @ Wed, 08 Dec 2021 21:09:34: 8000000 INFO @ Wed, 08 Dec 2021 21:09:36: 3000000 INFO @ Wed, 08 Dec 2021 21:09:38: 13000000 INFO @ Wed, 08 Dec 2021 21:09:40: 9000000 INFO @ Wed, 08 Dec 2021 21:09:43: 4000000 INFO @ Wed, 08 Dec 2021 21:09:44: 14000000 INFO @ Wed, 08 Dec 2021 21:09:46: 10000000 INFO @ Wed, 08 Dec 2021 21:09:49: 5000000 INFO @ Wed, 08 Dec 2021 21:09:51: 15000000 INFO @ Wed, 08 Dec 2021 21:09:52: 11000000 INFO @ Wed, 08 Dec 2021 21:09:56: 6000000 INFO @ Wed, 08 Dec 2021 21:09:57: 16000000 INFO @ Wed, 08 Dec 2021 21:09:58: 12000000 INFO @ Wed, 08 Dec 2021 21:10:02: 7000000 INFO @ Wed, 08 Dec 2021 21:10:04: 17000000 INFO @ Wed, 08 Dec 2021 21:10:04: 13000000 INFO @ Wed, 08 Dec 2021 21:10:09: 8000000 INFO @ Wed, 08 Dec 2021 21:10:10: 14000000 INFO @ Wed, 08 Dec 2021 21:10:10: 18000000 INFO @ Wed, 08 Dec 2021 21:10:15: 9000000 INFO @ Wed, 08 Dec 2021 21:10:16: 15000000 INFO @ Wed, 08 Dec 2021 21:10:17: 19000000 INFO @ Wed, 08 Dec 2021 21:10:22: 16000000 INFO @ Wed, 08 Dec 2021 21:10:22: 10000000 INFO @ Wed, 08 Dec 2021 21:10:24: 20000000 INFO @ Wed, 08 Dec 2021 21:10:27: 17000000 INFO @ Wed, 08 Dec 2021 21:10:29: 11000000 INFO @ Wed, 08 Dec 2021 21:10:30: 21000000 INFO @ Wed, 08 Dec 2021 21:10:33: 18000000 INFO @ Wed, 08 Dec 2021 21:10:35: 12000000 INFO @ Wed, 08 Dec 2021 21:10:37: 22000000 INFO @ Wed, 08 Dec 2021 21:10:39: 19000000 INFO @ Wed, 08 Dec 2021 21:10:41: 13000000 INFO @ Wed, 08 Dec 2021 21:10:43: 23000000 INFO @ Wed, 08 Dec 2021 21:10:46: 20000000 INFO @ Wed, 08 Dec 2021 21:10:48: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:10:50: 24000000 INFO @ Wed, 08 Dec 2021 21:10:50: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:10:50: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:10:50: #1 total tags in treatment: 11241262 INFO @ Wed, 08 Dec 2021 21:10:50: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:10:50: #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 21:10:50: #1 tags after filtering in treatment: 10562860 INFO @ Wed, 08 Dec 2021 21:10:50: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 21:10:50: #1 finished! INFO @ Wed, 08 Dec 2021 21:10:50: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:10:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:10:51: #2 number of paired peaks: 376 WARNING @ Wed, 08 Dec 2021 21:10:51: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Wed, 08 Dec 2021 21:10:51: start model_add_line... INFO @ Wed, 08 Dec 2021 21:10:51: start X-correlation... INFO @ Wed, 08 Dec 2021 21:10:51: end of X-cor INFO @ Wed, 08 Dec 2021 21:10:51: #2 finished! INFO @ Wed, 08 Dec 2021 21:10:51: #2 predicted fragment length is 144 bps INFO @ Wed, 08 Dec 2021 21:10:51: #2 alternative fragment length(s) may be 4,144 bps INFO @ Wed, 08 Dec 2021 21:10:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.05_model.r INFO @ Wed, 08 Dec 2021 21:10:51: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:10:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:10:51: 21000000 INFO @ Wed, 08 Dec 2021 21:10:54: 15000000 INFO @ Wed, 08 Dec 2021 21:10:57: 22000000 INFO @ Wed, 08 Dec 2021 21:11:01: 16000000 INFO @ Wed, 08 Dec 2021 21:11:03: 23000000 INFO @ Wed, 08 Dec 2021 21:11:07: 17000000 INFO @ Wed, 08 Dec 2021 21:11:08: 24000000 INFO @ Wed, 08 Dec 2021 21:11:09: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:11:09: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:11:09: #1 total tags in treatment: 11241262 INFO @ Wed, 08 Dec 2021 21:11:09: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:11:09: #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 21:11:09: #1 tags after filtering in treatment: 10562860 INFO @ Wed, 08 Dec 2021 21:11:09: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 21:11:09: #1 finished! INFO @ Wed, 08 Dec 2021 21:11:09: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:11:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:11:09: #2 number of paired peaks: 376 WARNING @ Wed, 08 Dec 2021 21:11:09: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Wed, 08 Dec 2021 21:11:09: start model_add_line... INFO @ Wed, 08 Dec 2021 21:11:09: start X-correlation... INFO @ Wed, 08 Dec 2021 21:11:09: end of X-cor INFO @ Wed, 08 Dec 2021 21:11:09: #2 finished! INFO @ Wed, 08 Dec 2021 21:11:09: #2 predicted fragment length is 144 bps INFO @ Wed, 08 Dec 2021 21:11:09: #2 alternative fragment length(s) may be 4,144 bps INFO @ Wed, 08 Dec 2021 21:11:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.10_model.r INFO @ Wed, 08 Dec 2021 21:11:10: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:11:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:11:11: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:11:13: 18000000 INFO @ Wed, 08 Dec 2021 21:11:19: 19000000 INFO @ Wed, 08 Dec 2021 21:11:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:11:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:11:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.05_summits.bed INFO @ Wed, 08 Dec 2021 21:11:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (335 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:11:25: 20000000 INFO @ Wed, 08 Dec 2021 21:11:29: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:11:31: 21000000 INFO @ Wed, 08 Dec 2021 21:11:37: 22000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:11:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:11:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:11:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.10_summits.bed INFO @ Wed, 08 Dec 2021 21:11:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (234 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:11:43: 23000000 INFO @ Wed, 08 Dec 2021 21:11:48: 24000000 INFO @ Wed, 08 Dec 2021 21:11:49: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:11:49: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:11:49: #1 total tags in treatment: 11241262 INFO @ Wed, 08 Dec 2021 21:11:49: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:11:49: #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 21:11:49: #1 tags after filtering in treatment: 10562860 INFO @ Wed, 08 Dec 2021 21:11:49: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 21:11:49: #1 finished! INFO @ Wed, 08 Dec 2021 21:11:49: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:11:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:11:49: #2 number of paired peaks: 376 WARNING @ Wed, 08 Dec 2021 21:11:49: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Wed, 08 Dec 2021 21:11:49: start model_add_line... INFO @ Wed, 08 Dec 2021 21:11:49: start X-correlation... INFO @ Wed, 08 Dec 2021 21:11:49: end of X-cor INFO @ Wed, 08 Dec 2021 21:11:49: #2 finished! INFO @ Wed, 08 Dec 2021 21:11:49: #2 predicted fragment length is 144 bps INFO @ Wed, 08 Dec 2021 21:11:49: #2 alternative fragment length(s) may be 4,144 bps INFO @ Wed, 08 Dec 2021 21:11:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.20_model.r INFO @ Wed, 08 Dec 2021 21:11:50: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:11:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:12:10: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:12:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:12:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:12:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976729/SRX8976729.20_summits.bed INFO @ Wed, 08 Dec 2021 21:12:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (170 records, 4 fields): 2 millis CompletedMACS2peakCalling