Job ID = 14160468 SRX = SRX9555455 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: 00:17:03 21504004 reads; of these: 21504004 (100.00%) were paired; of these: 1867283 (8.68%) aligned concordantly 0 times 17035684 (79.22%) aligned concordantly exactly 1 time 2601037 (12.10%) aligned concordantly >1 times ---- 1867283 pairs aligned concordantly 0 times; of these: 640425 (34.30%) aligned discordantly 1 time ---- 1226858 pairs aligned 0 times concordantly or discordantly; of these: 2453716 mates make up the pairs; of these: 1858418 (75.74%) aligned 0 times 392692 (16.00%) aligned exactly 1 time 202606 (8.26%) aligned >1 times 95.68% overall alignment rate Time searching: 00:17:03 Overall time: 00:17:03 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 20 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] 1346742 / 20246098 = 0.0665 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 03:06:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.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 03:06:47: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:06:47: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:06:51: 1000000 INFO @ Thu, 09 Dec 2021 03:06:55: 2000000 INFO @ Thu, 09 Dec 2021 03:06:59: 3000000 INFO @ Thu, 09 Dec 2021 03:07:03: 4000000 INFO @ Thu, 09 Dec 2021 03:07:07: 5000000 INFO @ Thu, 09 Dec 2021 03:07:11: 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 03:07:15: 7000000 INFO @ Thu, 09 Dec 2021 03:07:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.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 03:07:17: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:07:17: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:07:19: 8000000 INFO @ Thu, 09 Dec 2021 03:07:21: 1000000 INFO @ Thu, 09 Dec 2021 03:07:23: 9000000 INFO @ Thu, 09 Dec 2021 03:07:25: 2000000 INFO @ Thu, 09 Dec 2021 03:07:28: 10000000 INFO @ Thu, 09 Dec 2021 03:07:29: 3000000 INFO @ Thu, 09 Dec 2021 03:07:32: 11000000 INFO @ Thu, 09 Dec 2021 03:07:33: 4000000 INFO @ Thu, 09 Dec 2021 03:07:36: 12000000 INFO @ Thu, 09 Dec 2021 03:07:38: 5000000 INFO @ Thu, 09 Dec 2021 03:07:40: 13000000 INFO @ Thu, 09 Dec 2021 03:07:42: 6000000 INFO @ Thu, 09 Dec 2021 03:07:44: 14000000 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 03:07:46: 7000000 INFO @ Thu, 09 Dec 2021 03:07:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.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 03:07:47: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:07:47: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:07:48: 15000000 INFO @ Thu, 09 Dec 2021 03:07:50: 8000000 INFO @ Thu, 09 Dec 2021 03:07:52: 1000000 INFO @ Thu, 09 Dec 2021 03:07:52: 16000000 INFO @ Thu, 09 Dec 2021 03:07:54: 9000000 INFO @ Thu, 09 Dec 2021 03:07:56: 17000000 INFO @ Thu, 09 Dec 2021 03:07:57: 2000000 INFO @ Thu, 09 Dec 2021 03:07:58: 10000000 INFO @ Thu, 09 Dec 2021 03:08:01: 18000000 INFO @ Thu, 09 Dec 2021 03:08:02: 3000000 INFO @ Thu, 09 Dec 2021 03:08:02: 11000000 INFO @ Thu, 09 Dec 2021 03:08:05: 19000000 INFO @ Thu, 09 Dec 2021 03:08:07: 4000000 INFO @ Thu, 09 Dec 2021 03:08:07: 12000000 INFO @ Thu, 09 Dec 2021 03:08:09: 20000000 INFO @ Thu, 09 Dec 2021 03:08:11: 13000000 INFO @ Thu, 09 Dec 2021 03:08:11: 5000000 INFO @ Thu, 09 Dec 2021 03:08:13: 21000000 INFO @ Thu, 09 Dec 2021 03:08:15: 14000000 INFO @ Thu, 09 Dec 2021 03:08:16: 6000000 INFO @ Thu, 09 Dec 2021 03:08:17: 22000000 INFO @ Thu, 09 Dec 2021 03:08:19: 15000000 INFO @ Thu, 09 Dec 2021 03:08:21: 7000000 INFO @ Thu, 09 Dec 2021 03:08:21: 23000000 INFO @ Thu, 09 Dec 2021 03:08:23: 16000000 INFO @ Thu, 09 Dec 2021 03:08:26: 24000000 INFO @ Thu, 09 Dec 2021 03:08:26: 8000000 INFO @ Thu, 09 Dec 2021 03:08:28: 17000000 INFO @ Thu, 09 Dec 2021 03:08:30: 25000000 INFO @ Thu, 09 Dec 2021 03:08:30: 9000000 INFO @ Thu, 09 Dec 2021 03:08:32: 18000000 INFO @ Thu, 09 Dec 2021 03:08:34: 26000000 INFO @ Thu, 09 Dec 2021 03:08:35: 10000000 INFO @ Thu, 09 Dec 2021 03:08:36: 19000000 INFO @ Thu, 09 Dec 2021 03:08:38: 27000000 INFO @ Thu, 09 Dec 2021 03:08:40: 11000000 INFO @ Thu, 09 Dec 2021 03:08:40: 20000000 INFO @ Thu, 09 Dec 2021 03:08:42: 28000000 INFO @ Thu, 09 Dec 2021 03:08:44: 21000000 INFO @ Thu, 09 Dec 2021 03:08:45: 12000000 INFO @ Thu, 09 Dec 2021 03:08:46: 29000000 INFO @ Thu, 09 Dec 2021 03:08:49: 22000000 INFO @ Thu, 09 Dec 2021 03:08:50: 13000000 INFO @ Thu, 09 Dec 2021 03:08:50: 30000000 INFO @ Thu, 09 Dec 2021 03:08:53: 23000000 INFO @ Thu, 09 Dec 2021 03:08:54: 14000000 INFO @ Thu, 09 Dec 2021 03:08:55: 31000000 INFO @ Thu, 09 Dec 2021 03:08:57: 24000000 INFO @ Thu, 09 Dec 2021 03:08:59: 32000000 INFO @ Thu, 09 Dec 2021 03:08:59: 15000000 INFO @ Thu, 09 Dec 2021 03:09:01: 25000000 INFO @ Thu, 09 Dec 2021 03:09:03: 33000000 INFO @ Thu, 09 Dec 2021 03:09:04: 16000000 INFO @ Thu, 09 Dec 2021 03:09:05: 26000000 INFO @ Thu, 09 Dec 2021 03:09:07: 34000000 INFO @ Thu, 09 Dec 2021 03:09:09: 17000000 INFO @ Thu, 09 Dec 2021 03:09:10: 27000000 INFO @ Thu, 09 Dec 2021 03:09:11: 35000000 INFO @ Thu, 09 Dec 2021 03:09:13: 18000000 INFO @ Thu, 09 Dec 2021 03:09:14: 28000000 INFO @ Thu, 09 Dec 2021 03:09:15: 36000000 INFO @ Thu, 09 Dec 2021 03:09:18: 29000000 INFO @ Thu, 09 Dec 2021 03:09:18: 19000000 INFO @ Thu, 09 Dec 2021 03:09:20: 37000000 INFO @ Thu, 09 Dec 2021 03:09:22: 30000000 INFO @ Thu, 09 Dec 2021 03:09:23: 20000000 INFO @ Thu, 09 Dec 2021 03:09:24: 38000000 INFO @ Thu, 09 Dec 2021 03:09:26: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:09:26: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:09:26: #1 total tags in treatment: 18312564 INFO @ Thu, 09 Dec 2021 03:09:26: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:09:26: #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 03:09:26: #1 tags after filtering in treatment: 16633916 INFO @ Thu, 09 Dec 2021 03:09:26: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 09 Dec 2021 03:09:26: #1 finished! INFO @ Thu, 09 Dec 2021 03:09:26: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:09:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:09:26: 31000000 INFO @ Thu, 09 Dec 2021 03:09:27: #2 number of paired peaks: 305 WARNING @ Thu, 09 Dec 2021 03:09:27: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Thu, 09 Dec 2021 03:09:27: start model_add_line... INFO @ Thu, 09 Dec 2021 03:09:27: start X-correlation... INFO @ Thu, 09 Dec 2021 03:09:27: end of X-cor INFO @ Thu, 09 Dec 2021 03:09:27: #2 finished! INFO @ Thu, 09 Dec 2021 03:09:27: #2 predicted fragment length is 122 bps INFO @ Thu, 09 Dec 2021 03:09:27: #2 alternative fragment length(s) may be 3,122,125 bps INFO @ Thu, 09 Dec 2021 03:09:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.05_model.r INFO @ Thu, 09 Dec 2021 03:09:27: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:09:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:09:28: 21000000 INFO @ Thu, 09 Dec 2021 03:09:30: 32000000 INFO @ Thu, 09 Dec 2021 03:09:33: 22000000 INFO @ Thu, 09 Dec 2021 03:09:35: 33000000 INFO @ Thu, 09 Dec 2021 03:09:38: 23000000 INFO @ Thu, 09 Dec 2021 03:09:39: 34000000 INFO @ Thu, 09 Dec 2021 03:09:43: 35000000 INFO @ Thu, 09 Dec 2021 03:09:43: 24000000 INFO @ Thu, 09 Dec 2021 03:09:47: 36000000 INFO @ Thu, 09 Dec 2021 03:09:48: 25000000 INFO @ Thu, 09 Dec 2021 03:09:51: 37000000 INFO @ Thu, 09 Dec 2021 03:09:53: 26000000 INFO @ Thu, 09 Dec 2021 03:09:55: 38000000 INFO @ Thu, 09 Dec 2021 03:09:56: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:09:57: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:09:57: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:09:57: #1 total tags in treatment: 18312564 INFO @ Thu, 09 Dec 2021 03:09:57: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:09:57: #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 03:09:58: #1 tags after filtering in treatment: 16633916 INFO @ Thu, 09 Dec 2021 03:09:58: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 09 Dec 2021 03:09:58: #1 finished! INFO @ Thu, 09 Dec 2021 03:09:58: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:09:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:09:58: 27000000 INFO @ Thu, 09 Dec 2021 03:09:59: #2 number of paired peaks: 305 WARNING @ Thu, 09 Dec 2021 03:09:59: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Thu, 09 Dec 2021 03:09:59: start model_add_line... INFO @ Thu, 09 Dec 2021 03:09:59: start X-correlation... INFO @ Thu, 09 Dec 2021 03:09:59: end of X-cor INFO @ Thu, 09 Dec 2021 03:09:59: #2 finished! INFO @ Thu, 09 Dec 2021 03:09:59: #2 predicted fragment length is 122 bps INFO @ Thu, 09 Dec 2021 03:09:59: #2 alternative fragment length(s) may be 3,122,125 bps INFO @ Thu, 09 Dec 2021 03:09:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.10_model.r INFO @ Thu, 09 Dec 2021 03:09:59: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:09:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:10:03: 28000000 INFO @ Thu, 09 Dec 2021 03:10:08: 29000000 INFO @ Thu, 09 Dec 2021 03:10:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:10:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:10:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.05_summits.bed INFO @ Thu, 09 Dec 2021 03:10:09: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (423 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:10:13: 30000000 INFO @ Thu, 09 Dec 2021 03:10:18: 31000000 INFO @ Thu, 09 Dec 2021 03:10:23: 32000000 INFO @ Thu, 09 Dec 2021 03:10:27: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:10:28: 33000000 INFO @ Thu, 09 Dec 2021 03:10:33: 34000000 INFO @ Thu, 09 Dec 2021 03:10:37: 35000000 INFO @ Thu, 09 Dec 2021 03:10:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:10:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:10:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.10_summits.bed INFO @ Thu, 09 Dec 2021 03:10:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (327 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:10:42: 36000000 INFO @ Thu, 09 Dec 2021 03:10:47: 37000000 INFO @ Thu, 09 Dec 2021 03:10:52: 38000000 INFO @ Thu, 09 Dec 2021 03:10:55: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:10:55: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:10:55: #1 total tags in treatment: 18312564 INFO @ Thu, 09 Dec 2021 03:10:55: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:10:55: #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 03:10:55: #1 tags after filtering in treatment: 16633916 INFO @ Thu, 09 Dec 2021 03:10:55: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 09 Dec 2021 03:10:55: #1 finished! INFO @ Thu, 09 Dec 2021 03:10:55: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:10:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:10:56: #2 number of paired peaks: 305 WARNING @ Thu, 09 Dec 2021 03:10:56: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Thu, 09 Dec 2021 03:10:56: start model_add_line... INFO @ Thu, 09 Dec 2021 03:10:56: start X-correlation... INFO @ Thu, 09 Dec 2021 03:10:56: end of X-cor INFO @ Thu, 09 Dec 2021 03:10:56: #2 finished! INFO @ Thu, 09 Dec 2021 03:10:56: #2 predicted fragment length is 122 bps INFO @ Thu, 09 Dec 2021 03:10:56: #2 alternative fragment length(s) may be 3,122,125 bps INFO @ Thu, 09 Dec 2021 03:10:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.20_model.r INFO @ Thu, 09 Dec 2021 03:10:56: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:10:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:11:24: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:11:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:11:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:11:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9555455/SRX9555455.20_summits.bed INFO @ Thu, 09 Dec 2021 03:11:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (215 records, 4 fields): 1 millis CompletedMACS2peakCalling