Job ID = 14159636 SRX = SRX8976691 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: 00:13:30 16049738 reads; of these: 16049738 (100.00%) were paired; of these: 1888433 (11.77%) aligned concordantly 0 times 11404518 (71.06%) aligned concordantly exactly 1 time 2756787 (17.18%) aligned concordantly >1 times ---- 1888433 pairs aligned concordantly 0 times; of these: 1190130 (63.02%) aligned discordantly 1 time ---- 698303 pairs aligned 0 times concordantly or discordantly; of these: 1396606 mates make up the pairs; of these: 472751 (33.85%) aligned 0 times 323721 (23.18%) aligned exactly 1 time 600134 (42.97%) aligned >1 times 98.53% overall alignment rate Time searching: 00:13:30 Overall time: 00:13:30 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] 1285563 / 15339193 = 0.0838 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 00:00:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.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 00:00:19: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:00:19: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:00:23: 1000000 INFO @ Thu, 09 Dec 2021 00:00:27: 2000000 INFO @ Thu, 09 Dec 2021 00:00:31: 3000000 INFO @ Thu, 09 Dec 2021 00:00:35: 4000000 INFO @ Thu, 09 Dec 2021 00:00:39: 5000000 INFO @ Thu, 09 Dec 2021 00:00:44: 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 00:00:48: 7000000 INFO @ Thu, 09 Dec 2021 00:00:52: 8000000 INFO @ Thu, 09 Dec 2021 00:00:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.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 00:00:53: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:00:53: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:00:56: 9000000 INFO @ Thu, 09 Dec 2021 00:00:57: 1000000 INFO @ Thu, 09 Dec 2021 00:01:01: 10000000 INFO @ Thu, 09 Dec 2021 00:01:02: 2000000 INFO @ Thu, 09 Dec 2021 00:01:05: 11000000 INFO @ Thu, 09 Dec 2021 00:01:06: 3000000 INFO @ Thu, 09 Dec 2021 00:01:10: 12000000 INFO @ Thu, 09 Dec 2021 00:01:10: 4000000 INFO @ Thu, 09 Dec 2021 00:01:14: 13000000 INFO @ Thu, 09 Dec 2021 00:01:15: 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 00:01:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.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 00:01:18: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:01:18: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:01:19: 14000000 INFO @ Thu, 09 Dec 2021 00:01:19: 6000000 INFO @ Thu, 09 Dec 2021 00:01:23: 15000000 INFO @ Thu, 09 Dec 2021 00:01:24: 1000000 INFO @ Thu, 09 Dec 2021 00:01:24: 7000000 INFO @ Thu, 09 Dec 2021 00:01:28: 16000000 INFO @ Thu, 09 Dec 2021 00:01:29: 8000000 INFO @ Thu, 09 Dec 2021 00:01:29: 2000000 INFO @ Thu, 09 Dec 2021 00:01:33: 17000000 INFO @ Thu, 09 Dec 2021 00:01:34: 9000000 INFO @ Thu, 09 Dec 2021 00:01:34: 3000000 INFO @ Thu, 09 Dec 2021 00:01:37: 18000000 INFO @ Thu, 09 Dec 2021 00:01:38: 10000000 INFO @ Thu, 09 Dec 2021 00:01:40: 4000000 INFO @ Thu, 09 Dec 2021 00:01:42: 19000000 INFO @ Thu, 09 Dec 2021 00:01:43: 11000000 INFO @ Thu, 09 Dec 2021 00:01:45: 5000000 INFO @ Thu, 09 Dec 2021 00:01:47: 20000000 INFO @ Thu, 09 Dec 2021 00:01:48: 12000000 INFO @ Thu, 09 Dec 2021 00:01:51: 6000000 INFO @ Thu, 09 Dec 2021 00:01:52: 21000000 INFO @ Thu, 09 Dec 2021 00:01:53: 13000000 INFO @ Thu, 09 Dec 2021 00:01:56: 7000000 INFO @ Thu, 09 Dec 2021 00:01:56: 22000000 INFO @ Thu, 09 Dec 2021 00:01:57: 14000000 INFO @ Thu, 09 Dec 2021 00:02:01: 23000000 INFO @ Thu, 09 Dec 2021 00:02:01: 8000000 INFO @ Thu, 09 Dec 2021 00:02:02: 15000000 INFO @ Thu, 09 Dec 2021 00:02:06: 24000000 INFO @ Thu, 09 Dec 2021 00:02:07: 16000000 INFO @ Thu, 09 Dec 2021 00:02:07: 9000000 INFO @ Thu, 09 Dec 2021 00:02:11: 25000000 INFO @ Thu, 09 Dec 2021 00:02:12: 17000000 INFO @ Thu, 09 Dec 2021 00:02:12: 10000000 INFO @ Thu, 09 Dec 2021 00:02:15: 26000000 INFO @ Thu, 09 Dec 2021 00:02:16: 18000000 INFO @ Thu, 09 Dec 2021 00:02:18: 11000000 INFO @ Thu, 09 Dec 2021 00:02:20: 27000000 INFO @ Thu, 09 Dec 2021 00:02:21: 19000000 INFO @ Thu, 09 Dec 2021 00:02:23: 12000000 INFO @ Thu, 09 Dec 2021 00:02:25: 28000000 INFO @ Thu, 09 Dec 2021 00:02:26: 20000000 INFO @ Thu, 09 Dec 2021 00:02:29: 13000000 INFO @ Thu, 09 Dec 2021 00:02:30: 29000000 INFO @ Thu, 09 Dec 2021 00:02:30: #1 tag size is determined as 42 bps INFO @ Thu, 09 Dec 2021 00:02:30: #1 tag size = 42 INFO @ Thu, 09 Dec 2021 00:02:30: #1 total tags in treatment: 12949684 INFO @ Thu, 09 Dec 2021 00:02:30: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:02:30: #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 00:02:30: #1 tags after filtering in treatment: 11427687 INFO @ Thu, 09 Dec 2021 00:02:30: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 09 Dec 2021 00:02:30: #1 finished! INFO @ Thu, 09 Dec 2021 00:02:30: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:02:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:02:31: 21000000 INFO @ Thu, 09 Dec 2021 00:02:31: #2 number of paired peaks: 609 WARNING @ Thu, 09 Dec 2021 00:02:31: Fewer paired peaks (609) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 609 pairs to build model! INFO @ Thu, 09 Dec 2021 00:02:31: start model_add_line... INFO @ Thu, 09 Dec 2021 00:02:31: start X-correlation... INFO @ Thu, 09 Dec 2021 00:02:31: end of X-cor INFO @ Thu, 09 Dec 2021 00:02:31: #2 finished! INFO @ Thu, 09 Dec 2021 00:02:31: #2 predicted fragment length is 143 bps INFO @ Thu, 09 Dec 2021 00:02:31: #2 alternative fragment length(s) may be 3,143 bps INFO @ Thu, 09 Dec 2021 00:02:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.05_model.r INFO @ Thu, 09 Dec 2021 00:02:31: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:02:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:02:34: 14000000 INFO @ Thu, 09 Dec 2021 00:02:35: 22000000 INFO @ Thu, 09 Dec 2021 00:02:39: 15000000 INFO @ Thu, 09 Dec 2021 00:02:40: 23000000 INFO @ Thu, 09 Dec 2021 00:02:45: 24000000 INFO @ Thu, 09 Dec 2021 00:02:45: 16000000 INFO @ Thu, 09 Dec 2021 00:02:49: 25000000 INFO @ Thu, 09 Dec 2021 00:02:50: 17000000 INFO @ Thu, 09 Dec 2021 00:02:54: 26000000 INFO @ Thu, 09 Dec 2021 00:02:55: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:02:55: 18000000 INFO @ Thu, 09 Dec 2021 00:02:59: 27000000 INFO @ Thu, 09 Dec 2021 00:03:01: 19000000 INFO @ Thu, 09 Dec 2021 00:03:03: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:03:06: 20000000 INFO @ Thu, 09 Dec 2021 00:03:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:03:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:03:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.05_summits.bed INFO @ Thu, 09 Dec 2021 00:03:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (546 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:03:08: 29000000 INFO @ Thu, 09 Dec 2021 00:03:08: #1 tag size is determined as 42 bps INFO @ Thu, 09 Dec 2021 00:03:08: #1 tag size = 42 INFO @ Thu, 09 Dec 2021 00:03:08: #1 total tags in treatment: 12949684 INFO @ Thu, 09 Dec 2021 00:03:08: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:03:08: #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 00:03:09: #1 tags after filtering in treatment: 11427687 INFO @ Thu, 09 Dec 2021 00:03:09: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 09 Dec 2021 00:03:09: #1 finished! INFO @ Thu, 09 Dec 2021 00:03:09: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:03:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:03:09: #2 number of paired peaks: 609 WARNING @ Thu, 09 Dec 2021 00:03:09: Fewer paired peaks (609) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 609 pairs to build model! INFO @ Thu, 09 Dec 2021 00:03:09: start model_add_line... INFO @ Thu, 09 Dec 2021 00:03:09: start X-correlation... INFO @ Thu, 09 Dec 2021 00:03:09: end of X-cor INFO @ Thu, 09 Dec 2021 00:03:09: #2 finished! INFO @ Thu, 09 Dec 2021 00:03:09: #2 predicted fragment length is 143 bps INFO @ Thu, 09 Dec 2021 00:03:09: #2 alternative fragment length(s) may be 3,143 bps INFO @ Thu, 09 Dec 2021 00:03:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.10_model.r INFO @ Thu, 09 Dec 2021 00:03:09: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:03:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:03:11: 21000000 INFO @ Thu, 09 Dec 2021 00:03:16: 22000000 INFO @ Thu, 09 Dec 2021 00:03:21: 23000000 INFO @ Thu, 09 Dec 2021 00:03:26: 24000000 INFO @ Thu, 09 Dec 2021 00:03:31: 25000000 INFO @ Thu, 09 Dec 2021 00:03:33: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:03:36: 26000000 INFO @ Thu, 09 Dec 2021 00:03:41: 27000000 INFO @ Thu, 09 Dec 2021 00:03:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:03:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:03:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.10_summits.bed INFO @ Thu, 09 Dec 2021 00:03:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (297 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:03:46: 28000000 INFO @ Thu, 09 Dec 2021 00:03:51: 29000000 INFO @ Thu, 09 Dec 2021 00:03:51: #1 tag size is determined as 42 bps INFO @ Thu, 09 Dec 2021 00:03:51: #1 tag size = 42 INFO @ Thu, 09 Dec 2021 00:03:51: #1 total tags in treatment: 12949684 INFO @ Thu, 09 Dec 2021 00:03:51: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:03:51: #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 00:03:51: #1 tags after filtering in treatment: 11427687 INFO @ Thu, 09 Dec 2021 00:03:51: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 09 Dec 2021 00:03:51: #1 finished! INFO @ Thu, 09 Dec 2021 00:03:51: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:03:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:03:52: #2 number of paired peaks: 609 WARNING @ Thu, 09 Dec 2021 00:03:52: Fewer paired peaks (609) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 609 pairs to build model! INFO @ Thu, 09 Dec 2021 00:03:52: start model_add_line... INFO @ Thu, 09 Dec 2021 00:03:52: start X-correlation... INFO @ Thu, 09 Dec 2021 00:03:52: end of X-cor INFO @ Thu, 09 Dec 2021 00:03:52: #2 finished! INFO @ Thu, 09 Dec 2021 00:03:52: #2 predicted fragment length is 143 bps INFO @ Thu, 09 Dec 2021 00:03:52: #2 alternative fragment length(s) may be 3,143 bps INFO @ Thu, 09 Dec 2021 00:03:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.20_model.r INFO @ Thu, 09 Dec 2021 00:03:52: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:03:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:04:15: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:04:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:04:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:04:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976691/SRX8976691.20_summits.bed INFO @ Thu, 09 Dec 2021 00:04:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (212 records, 4 fields): 1 millis CompletedMACS2peakCalling