Job ID = 14159336 SRX = SRX8976735 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: 00:09:50 12863177 reads; of these: 12863177 (100.00%) were paired; of these: 1176097 (9.14%) aligned concordantly 0 times 10153493 (78.93%) aligned concordantly exactly 1 time 1533587 (11.92%) aligned concordantly >1 times ---- 1176097 pairs aligned concordantly 0 times; of these: 888720 (75.57%) aligned discordantly 1 time ---- 287377 pairs aligned 0 times concordantly or discordantly; of these: 574754 mates make up the pairs; of these: 148150 (25.78%) aligned 0 times 183417 (31.91%) aligned exactly 1 time 243187 (42.31%) aligned >1 times 99.42% overall alignment rate Time searching: 00:09:50 Overall time: 00:09:50 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] 360840 / 12549114 = 0.0288 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 21:14:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.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 21:14:09: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:14:09: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:14:16: 1000000 INFO @ Wed, 08 Dec 2021 21:14:22: 2000000 INFO @ Wed, 08 Dec 2021 21:14:29: 3000000 INFO @ Wed, 08 Dec 2021 21:14:35: 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 21:14:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.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 21:14:39: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:14:39: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:14:43: 5000000 INFO @ Wed, 08 Dec 2021 21:14:46: 1000000 INFO @ Wed, 08 Dec 2021 21:14:50: 6000000 INFO @ Wed, 08 Dec 2021 21:14:52: 2000000 INFO @ Wed, 08 Dec 2021 21:14:57: 7000000 INFO @ Wed, 08 Dec 2021 21:14:58: 3000000 INFO @ Wed, 08 Dec 2021 21:15:05: 4000000 INFO @ Wed, 08 Dec 2021 21:15:05: 8000000 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 21:15:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.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 21:15:09: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:15:09: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:15:11: 5000000 INFO @ Wed, 08 Dec 2021 21:15:13: 9000000 INFO @ Wed, 08 Dec 2021 21:15:17: 1000000 INFO @ Wed, 08 Dec 2021 21:15:18: 6000000 INFO @ Wed, 08 Dec 2021 21:15:20: 10000000 INFO @ Wed, 08 Dec 2021 21:15:24: 2000000 INFO @ Wed, 08 Dec 2021 21:15:24: 7000000 INFO @ Wed, 08 Dec 2021 21:15:28: 11000000 INFO @ Wed, 08 Dec 2021 21:15:31: 8000000 INFO @ Wed, 08 Dec 2021 21:15:32: 3000000 INFO @ Wed, 08 Dec 2021 21:15:35: 12000000 INFO @ Wed, 08 Dec 2021 21:15:37: 9000000 INFO @ Wed, 08 Dec 2021 21:15:39: 4000000 INFO @ Wed, 08 Dec 2021 21:15:43: 13000000 INFO @ Wed, 08 Dec 2021 21:15:44: 10000000 INFO @ Wed, 08 Dec 2021 21:15:47: 5000000 INFO @ Wed, 08 Dec 2021 21:15:50: 14000000 INFO @ Wed, 08 Dec 2021 21:15:51: 11000000 INFO @ Wed, 08 Dec 2021 21:15:54: 6000000 INFO @ Wed, 08 Dec 2021 21:15:57: 12000000 INFO @ Wed, 08 Dec 2021 21:15:58: 15000000 INFO @ Wed, 08 Dec 2021 21:16:02: 7000000 INFO @ Wed, 08 Dec 2021 21:16:04: 13000000 INFO @ Wed, 08 Dec 2021 21:16:06: 16000000 INFO @ Wed, 08 Dec 2021 21:16:09: 8000000 INFO @ Wed, 08 Dec 2021 21:16:10: 14000000 INFO @ Wed, 08 Dec 2021 21:16:13: 17000000 INFO @ Wed, 08 Dec 2021 21:16:17: 9000000 INFO @ Wed, 08 Dec 2021 21:16:17: 15000000 INFO @ Wed, 08 Dec 2021 21:16:21: 18000000 INFO @ Wed, 08 Dec 2021 21:16:23: 16000000 INFO @ Wed, 08 Dec 2021 21:16:24: 10000000 INFO @ Wed, 08 Dec 2021 21:16:29: 19000000 INFO @ Wed, 08 Dec 2021 21:16:30: 17000000 INFO @ Wed, 08 Dec 2021 21:16:32: 11000000 INFO @ Wed, 08 Dec 2021 21:16:36: 20000000 INFO @ Wed, 08 Dec 2021 21:16:36: 18000000 INFO @ Wed, 08 Dec 2021 21:16:39: 12000000 INFO @ Wed, 08 Dec 2021 21:16:43: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:16:44: 21000000 INFO @ Wed, 08 Dec 2021 21:16:47: 13000000 INFO @ Wed, 08 Dec 2021 21:16:50: 20000000 INFO @ Wed, 08 Dec 2021 21:16:51: 22000000 INFO @ Wed, 08 Dec 2021 21:16:54: 14000000 INFO @ Wed, 08 Dec 2021 21:16:56: 21000000 INFO @ Wed, 08 Dec 2021 21:16:59: 23000000 INFO @ Wed, 08 Dec 2021 21:17:02: 15000000 INFO @ Wed, 08 Dec 2021 21:17:03: 22000000 INFO @ Wed, 08 Dec 2021 21:17:07: 24000000 INFO @ Wed, 08 Dec 2021 21:17:09: 16000000 INFO @ Wed, 08 Dec 2021 21:17:09: 23000000 INFO @ Wed, 08 Dec 2021 21:17:13: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:17:13: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:17:13: #1 total tags in treatment: 11345499 INFO @ Wed, 08 Dec 2021 21:17:13: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:17:13: #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 21:17:13: #1 tags after filtering in treatment: 10633921 INFO @ Wed, 08 Dec 2021 21:17:13: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 21:17:13: #1 finished! INFO @ Wed, 08 Dec 2021 21:17:13: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:17:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:17:14: #2 number of paired peaks: 355 WARNING @ Wed, 08 Dec 2021 21:17:14: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Wed, 08 Dec 2021 21:17:14: start model_add_line... INFO @ Wed, 08 Dec 2021 21:17:14: start X-correlation... INFO @ Wed, 08 Dec 2021 21:17:14: end of X-cor INFO @ Wed, 08 Dec 2021 21:17:14: #2 finished! INFO @ Wed, 08 Dec 2021 21:17:14: #2 predicted fragment length is 177 bps INFO @ Wed, 08 Dec 2021 21:17:14: #2 alternative fragment length(s) may be 4,177 bps INFO @ Wed, 08 Dec 2021 21:17:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.05_model.r INFO @ Wed, 08 Dec 2021 21:17:14: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:17:14: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:17:16: 24000000 INFO @ Wed, 08 Dec 2021 21:17:17: 17000000 INFO @ Wed, 08 Dec 2021 21:17:21: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:17:21: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:17:21: #1 total tags in treatment: 11345499 INFO @ Wed, 08 Dec 2021 21:17:21: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:17:21: #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 21:17:22: #1 tags after filtering in treatment: 10633921 INFO @ Wed, 08 Dec 2021 21:17:22: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 21:17:22: #1 finished! INFO @ Wed, 08 Dec 2021 21:17:22: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:17:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:17:22: #2 number of paired peaks: 355 WARNING @ Wed, 08 Dec 2021 21:17:22: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Wed, 08 Dec 2021 21:17:22: start model_add_line... INFO @ Wed, 08 Dec 2021 21:17:22: start X-correlation... INFO @ Wed, 08 Dec 2021 21:17:22: end of X-cor INFO @ Wed, 08 Dec 2021 21:17:22: #2 finished! INFO @ Wed, 08 Dec 2021 21:17:22: #2 predicted fragment length is 177 bps INFO @ Wed, 08 Dec 2021 21:17:22: #2 alternative fragment length(s) may be 4,177 bps INFO @ Wed, 08 Dec 2021 21:17:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.10_model.r INFO @ Wed, 08 Dec 2021 21:17:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:17:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:17:24: 18000000 INFO @ Wed, 08 Dec 2021 21:17:31: 19000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:17:35: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:17:38: 20000000 INFO @ Wed, 08 Dec 2021 21:17:44: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:17:44: 21000000 INFO @ Wed, 08 Dec 2021 21:17:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:17:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:17:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.05_summits.bed INFO @ Wed, 08 Dec 2021 21:17:45: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (304 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:17:51: 22000000 INFO @ Wed, 08 Dec 2021 21:17:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:17:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:17:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.10_summits.bed INFO @ Wed, 08 Dec 2021 21:17:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (234 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:17:58: 23000000 INFO @ Wed, 08 Dec 2021 21:18:05: 24000000 INFO @ Wed, 08 Dec 2021 21:18:10: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:18:10: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:18:10: #1 total tags in treatment: 11345499 INFO @ Wed, 08 Dec 2021 21:18:10: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:18:10: #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 21:18:10: #1 tags after filtering in treatment: 10633921 INFO @ Wed, 08 Dec 2021 21:18:10: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 21:18:10: #1 finished! INFO @ Wed, 08 Dec 2021 21:18:10: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:18:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:18:11: #2 number of paired peaks: 355 WARNING @ Wed, 08 Dec 2021 21:18:11: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Wed, 08 Dec 2021 21:18:11: start model_add_line... INFO @ Wed, 08 Dec 2021 21:18:11: start X-correlation... INFO @ Wed, 08 Dec 2021 21:18:11: end of X-cor INFO @ Wed, 08 Dec 2021 21:18:11: #2 finished! INFO @ Wed, 08 Dec 2021 21:18:11: #2 predicted fragment length is 177 bps INFO @ Wed, 08 Dec 2021 21:18:11: #2 alternative fragment length(s) may be 4,177 bps INFO @ Wed, 08 Dec 2021 21:18:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.20_model.r INFO @ Wed, 08 Dec 2021 21:18:11: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:18:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:18:31: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:18:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:18:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:18:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976735/SRX8976735.20_summits.bed INFO @ Wed, 08 Dec 2021 21:18:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (163 records, 4 fields): 1 millis CompletedMACS2peakCalling