Job ID = 14159391 SRX = SRX8976741 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: 00:11:05 13655992 reads; of these: 13655992 (100.00%) were paired; of these: 1133569 (8.30%) aligned concordantly 0 times 10739377 (78.64%) aligned concordantly exactly 1 time 1783046 (13.06%) aligned concordantly >1 times ---- 1133569 pairs aligned concordantly 0 times; of these: 818036 (72.16%) aligned discordantly 1 time ---- 315533 pairs aligned 0 times concordantly or discordantly; of these: 631066 mates make up the pairs; of these: 190670 (30.21%) aligned 0 times 191030 (30.27%) aligned exactly 1 time 249366 (39.52%) aligned >1 times 99.30% overall alignment rate Time searching: 00:11:06 Overall time: 00:11:06 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] 381227 / 13307386 = 0.0286 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 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 21:49:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.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 21:49:10: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:49:10: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:49:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.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 21:49:10: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:49:10: #1 read treatment tags... 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 21:49:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.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 21:49:14: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:49:14: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:49:16: 1000000 INFO @ Wed, 08 Dec 2021 21:49:16: 1000000 INFO @ Wed, 08 Dec 2021 21:49:19: 1000000 INFO @ Wed, 08 Dec 2021 21:49:22: 2000000 INFO @ Wed, 08 Dec 2021 21:49:22: 2000000 INFO @ Wed, 08 Dec 2021 21:49:25: 2000000 INFO @ Wed, 08 Dec 2021 21:49:28: 3000000 INFO @ Wed, 08 Dec 2021 21:49:28: 3000000 INFO @ Wed, 08 Dec 2021 21:49:30: 3000000 INFO @ Wed, 08 Dec 2021 21:49:33: 4000000 INFO @ Wed, 08 Dec 2021 21:49:34: 4000000 INFO @ Wed, 08 Dec 2021 21:49:35: 4000000 INFO @ Wed, 08 Dec 2021 21:49:39: 5000000 INFO @ Wed, 08 Dec 2021 21:49:39: 5000000 INFO @ Wed, 08 Dec 2021 21:49:41: 5000000 INFO @ Wed, 08 Dec 2021 21:49:44: 6000000 INFO @ Wed, 08 Dec 2021 21:49:45: 6000000 INFO @ Wed, 08 Dec 2021 21:49:46: 6000000 INFO @ Wed, 08 Dec 2021 21:49:49: 7000000 INFO @ Wed, 08 Dec 2021 21:49:50: 7000000 INFO @ Wed, 08 Dec 2021 21:49:51: 7000000 INFO @ Wed, 08 Dec 2021 21:49:54: 8000000 INFO @ Wed, 08 Dec 2021 21:49:55: 8000000 INFO @ Wed, 08 Dec 2021 21:49:57: 8000000 INFO @ Wed, 08 Dec 2021 21:49:59: 9000000 INFO @ Wed, 08 Dec 2021 21:50:01: 9000000 INFO @ Wed, 08 Dec 2021 21:50:02: 9000000 INFO @ Wed, 08 Dec 2021 21:50:05: 10000000 INFO @ Wed, 08 Dec 2021 21:50:06: 10000000 INFO @ Wed, 08 Dec 2021 21:50:08: 10000000 INFO @ Wed, 08 Dec 2021 21:50:10: 11000000 INFO @ Wed, 08 Dec 2021 21:50:11: 11000000 INFO @ Wed, 08 Dec 2021 21:50:13: 11000000 INFO @ Wed, 08 Dec 2021 21:50:16: 12000000 INFO @ Wed, 08 Dec 2021 21:50:17: 12000000 INFO @ Wed, 08 Dec 2021 21:50:18: 12000000 INFO @ Wed, 08 Dec 2021 21:50:21: 13000000 INFO @ Wed, 08 Dec 2021 21:50:23: 13000000 INFO @ Wed, 08 Dec 2021 21:50:24: 13000000 INFO @ Wed, 08 Dec 2021 21:50:27: 14000000 INFO @ Wed, 08 Dec 2021 21:50:28: 14000000 INFO @ Wed, 08 Dec 2021 21:50:30: 14000000 INFO @ Wed, 08 Dec 2021 21:50:32: 15000000 INFO @ Wed, 08 Dec 2021 21:50:34: 15000000 INFO @ Wed, 08 Dec 2021 21:50:35: 15000000 INFO @ Wed, 08 Dec 2021 21:50:38: 16000000 INFO @ Wed, 08 Dec 2021 21:50:39: 16000000 INFO @ Wed, 08 Dec 2021 21:50:41: 16000000 INFO @ Wed, 08 Dec 2021 21:50:43: 17000000 INFO @ Wed, 08 Dec 2021 21:50:44: 17000000 INFO @ Wed, 08 Dec 2021 21:50:46: 17000000 INFO @ Wed, 08 Dec 2021 21:50:48: 18000000 INFO @ Wed, 08 Dec 2021 21:50:50: 18000000 INFO @ Wed, 08 Dec 2021 21:50:52: 18000000 INFO @ Wed, 08 Dec 2021 21:50:54: 19000000 BedGraph に変換しました。 INFO @ Wed, 08 Dec 2021 21:50:55: 19000000 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:50:57: 19000000 INFO @ Wed, 08 Dec 2021 21:50:59: 20000000 INFO @ Wed, 08 Dec 2021 21:51:00: 20000000 INFO @ Wed, 08 Dec 2021 21:51:03: 20000000 INFO @ Wed, 08 Dec 2021 21:51:05: 21000000 INFO @ Wed, 08 Dec 2021 21:51:06: 21000000 INFO @ Wed, 08 Dec 2021 21:51:08: 21000000 INFO @ Wed, 08 Dec 2021 21:51:10: 22000000 INFO @ Wed, 08 Dec 2021 21:51:11: 22000000 INFO @ Wed, 08 Dec 2021 21:51:14: 22000000 INFO @ Wed, 08 Dec 2021 21:51:15: 23000000 INFO @ Wed, 08 Dec 2021 21:51:16: 23000000 INFO @ Wed, 08 Dec 2021 21:51:19: 23000000 INFO @ Wed, 08 Dec 2021 21:51:21: 24000000 INFO @ Wed, 08 Dec 2021 21:51:22: 24000000 INFO @ Wed, 08 Dec 2021 21:51:25: 24000000 INFO @ Wed, 08 Dec 2021 21:51:26: 25000000 INFO @ Wed, 08 Dec 2021 21:51:27: 25000000 INFO @ Wed, 08 Dec 2021 21:51:30: 25000000 INFO @ Wed, 08 Dec 2021 21:51:32: 26000000 INFO @ Wed, 08 Dec 2021 21:51:33: 26000000 INFO @ Wed, 08 Dec 2021 21:51:33: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:51:33: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:51:33: #1 total tags in treatment: 12159060 INFO @ Wed, 08 Dec 2021 21:51:33: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:51:33: #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 21:51:34: #1 tags after filtering in treatment: 11310265 INFO @ Wed, 08 Dec 2021 21:51:34: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 21:51:34: #1 finished! INFO @ Wed, 08 Dec 2021 21:51:34: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:51:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:51:34: #2 number of paired peaks: 338 WARNING @ Wed, 08 Dec 2021 21:51:34: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Wed, 08 Dec 2021 21:51:34: start model_add_line... INFO @ Wed, 08 Dec 2021 21:51:34: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:51:34: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:51:34: #1 total tags in treatment: 12159060 INFO @ Wed, 08 Dec 2021 21:51:34: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:51:34: #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 21:51:35: start X-correlation... INFO @ Wed, 08 Dec 2021 21:51:35: end of X-cor INFO @ Wed, 08 Dec 2021 21:51:35: #2 finished! INFO @ Wed, 08 Dec 2021 21:51:35: #2 predicted fragment length is 160 bps INFO @ Wed, 08 Dec 2021 21:51:35: #2 alternative fragment length(s) may be 4,160 bps INFO @ Wed, 08 Dec 2021 21:51:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.10_model.r INFO @ Wed, 08 Dec 2021 21:51:35: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:51:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:51:35: #1 tags after filtering in treatment: 11310265 INFO @ Wed, 08 Dec 2021 21:51:35: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 21:51:35: #1 finished! INFO @ Wed, 08 Dec 2021 21:51:35: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:51:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:51:35: #2 number of paired peaks: 338 WARNING @ Wed, 08 Dec 2021 21:51:35: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Wed, 08 Dec 2021 21:51:35: start model_add_line... INFO @ Wed, 08 Dec 2021 21:51:35: 26000000 INFO @ Wed, 08 Dec 2021 21:51:35: start X-correlation... INFO @ Wed, 08 Dec 2021 21:51:35: end of X-cor INFO @ Wed, 08 Dec 2021 21:51:35: #2 finished! INFO @ Wed, 08 Dec 2021 21:51:35: #2 predicted fragment length is 160 bps INFO @ Wed, 08 Dec 2021 21:51:35: #2 alternative fragment length(s) may be 4,160 bps INFO @ Wed, 08 Dec 2021 21:51:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.05_model.r INFO @ Wed, 08 Dec 2021 21:51:35: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:51:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:51:37: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:51:37: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:51:37: #1 total tags in treatment: 12159060 INFO @ Wed, 08 Dec 2021 21:51:37: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:51:37: #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 21:51:37: #1 tags after filtering in treatment: 11310265 INFO @ Wed, 08 Dec 2021 21:51:37: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 21:51:37: #1 finished! INFO @ Wed, 08 Dec 2021 21:51:37: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:51:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:51:38: #2 number of paired peaks: 338 WARNING @ Wed, 08 Dec 2021 21:51:38: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Wed, 08 Dec 2021 21:51:38: start model_add_line... INFO @ Wed, 08 Dec 2021 21:51:38: start X-correlation... INFO @ Wed, 08 Dec 2021 21:51:38: end of X-cor INFO @ Wed, 08 Dec 2021 21:51:38: #2 finished! INFO @ Wed, 08 Dec 2021 21:51:38: #2 predicted fragment length is 160 bps INFO @ Wed, 08 Dec 2021 21:51:38: #2 alternative fragment length(s) may be 4,160 bps INFO @ Wed, 08 Dec 2021 21:51:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.20_model.r INFO @ Wed, 08 Dec 2021 21:51:38: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:51:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:51:57: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:51:57: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:52:01: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:52:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:52:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:52:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.10_summits.bed INFO @ Wed, 08 Dec 2021 21:52:11: Done! INFO @ Wed, 08 Dec 2021 21:52:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:52:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:52:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.05_summits.bed INFO @ Wed, 08 Dec 2021 21:52:11: Done! INFO @ Wed, 08 Dec 2021 21:52:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:52:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:52:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976741/SRX8976741.20_summits.bed INFO @ Wed, 08 Dec 2021 21:52:13: Done! pass1 - making usageList (7 chroms): 1 millis pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (181 records, 4 fields): 1 millis pass2 - checking and writing primary data (343 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (254 records, 4 fields): 1 millis CompletedMACS2peakCalling