Job ID = 14159950 SRX = SRX8845643 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: 00:37:49 34620754 reads; of these: 34620754 (100.00%) were paired; of these: 20032188 (57.86%) aligned concordantly 0 times 12490475 (36.08%) aligned concordantly exactly 1 time 2098091 (6.06%) aligned concordantly >1 times ---- 20032188 pairs aligned concordantly 0 times; of these: 2002394 (10.00%) aligned discordantly 1 time ---- 18029794 pairs aligned 0 times concordantly or discordantly; of these: 36059588 mates make up the pairs; of these: 34714982 (96.27%) aligned 0 times 375885 (1.04%) aligned exactly 1 time 968721 (2.69%) aligned >1 times 49.86% overall alignment rate Time searching: 00:37:49 Overall time: 00:37:49 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 24 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] 3058962 / 16527425 = 0.1851 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 01:30:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.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 01:30:15: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:30:15: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:30:21: 1000000 INFO @ Thu, 09 Dec 2021 01:30:26: 2000000 INFO @ Thu, 09 Dec 2021 01:30:32: 3000000 INFO @ Thu, 09 Dec 2021 01:30:37: 4000000 INFO @ Thu, 09 Dec 2021 01:30:43: 5000000 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 01:30:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.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 01:30:45: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:30:45: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:30:48: 6000000 INFO @ Thu, 09 Dec 2021 01:30:51: 1000000 INFO @ Thu, 09 Dec 2021 01:30:54: 7000000 INFO @ Thu, 09 Dec 2021 01:30:57: 2000000 INFO @ Thu, 09 Dec 2021 01:30:59: 8000000 INFO @ Thu, 09 Dec 2021 01:31:02: 3000000 INFO @ Thu, 09 Dec 2021 01:31:05: 9000000 INFO @ Thu, 09 Dec 2021 01:31:08: 4000000 INFO @ Thu, 09 Dec 2021 01:31:10: 10000000 INFO @ Thu, 09 Dec 2021 01:31:13: 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 01:31:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.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 01:31:16: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:31:16: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:31:16: 11000000 INFO @ Thu, 09 Dec 2021 01:31:19: 6000000 INFO @ Thu, 09 Dec 2021 01:31:21: 1000000 INFO @ Thu, 09 Dec 2021 01:31:22: 12000000 INFO @ Thu, 09 Dec 2021 01:31:25: 7000000 INFO @ Thu, 09 Dec 2021 01:31:27: 2000000 INFO @ Thu, 09 Dec 2021 01:31:27: 13000000 INFO @ Thu, 09 Dec 2021 01:31:31: 8000000 INFO @ Thu, 09 Dec 2021 01:31:33: 14000000 INFO @ Thu, 09 Dec 2021 01:31:33: 3000000 INFO @ Thu, 09 Dec 2021 01:31:37: 9000000 INFO @ Thu, 09 Dec 2021 01:31:39: 15000000 INFO @ Thu, 09 Dec 2021 01:31:39: 4000000 INFO @ Thu, 09 Dec 2021 01:31:43: 10000000 INFO @ Thu, 09 Dec 2021 01:31:44: 16000000 INFO @ Thu, 09 Dec 2021 01:31:45: 5000000 INFO @ Thu, 09 Dec 2021 01:31:49: 11000000 INFO @ Thu, 09 Dec 2021 01:31:50: 17000000 INFO @ Thu, 09 Dec 2021 01:31:51: 6000000 INFO @ Thu, 09 Dec 2021 01:31:54: 12000000 INFO @ Thu, 09 Dec 2021 01:31:56: 18000000 INFO @ Thu, 09 Dec 2021 01:31:56: 7000000 INFO @ Thu, 09 Dec 2021 01:32:00: 13000000 INFO @ Thu, 09 Dec 2021 01:32:01: 19000000 INFO @ Thu, 09 Dec 2021 01:32:02: 8000000 INFO @ Thu, 09 Dec 2021 01:32:06: 14000000 INFO @ Thu, 09 Dec 2021 01:32:07: 20000000 INFO @ Thu, 09 Dec 2021 01:32:08: 9000000 INFO @ Thu, 09 Dec 2021 01:32:12: 15000000 INFO @ Thu, 09 Dec 2021 01:32:12: 21000000 INFO @ Thu, 09 Dec 2021 01:32:14: 10000000 INFO @ Thu, 09 Dec 2021 01:32:18: 22000000 INFO @ Thu, 09 Dec 2021 01:32:18: 16000000 INFO @ Thu, 09 Dec 2021 01:32:20: 11000000 INFO @ Thu, 09 Dec 2021 01:32:23: 23000000 INFO @ Thu, 09 Dec 2021 01:32:24: 17000000 INFO @ Thu, 09 Dec 2021 01:32:26: 12000000 INFO @ Thu, 09 Dec 2021 01:32:29: 24000000 INFO @ Thu, 09 Dec 2021 01:32:30: 18000000 INFO @ Thu, 09 Dec 2021 01:32:31: 13000000 INFO @ Thu, 09 Dec 2021 01:32:34: 25000000 INFO @ Thu, 09 Dec 2021 01:32:36: 19000000 INFO @ Thu, 09 Dec 2021 01:32:37: 14000000 INFO @ Thu, 09 Dec 2021 01:32:40: 26000000 INFO @ Thu, 09 Dec 2021 01:32:42: 20000000 INFO @ Thu, 09 Dec 2021 01:32:43: 15000000 INFO @ Thu, 09 Dec 2021 01:32:45: 27000000 INFO @ Thu, 09 Dec 2021 01:32:48: 21000000 INFO @ Thu, 09 Dec 2021 01:32:49: 16000000 INFO @ Thu, 09 Dec 2021 01:32:51: 28000000 INFO @ Thu, 09 Dec 2021 01:32:53: #1 tag size is determined as 125 bps INFO @ Thu, 09 Dec 2021 01:32:53: #1 tag size = 125 INFO @ Thu, 09 Dec 2021 01:32:53: #1 total tags in treatment: 11893730 INFO @ Thu, 09 Dec 2021 01:32:53: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:32:53: #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 01:32:53: #1 tags after filtering in treatment: 8227587 INFO @ Thu, 09 Dec 2021 01:32:53: #1 Redundant rate of treatment: 0.31 INFO @ Thu, 09 Dec 2021 01:32:53: #1 finished! INFO @ Thu, 09 Dec 2021 01:32:53: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:32:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:32:54: 22000000 INFO @ Thu, 09 Dec 2021 01:32:54: #2 number of paired peaks: 965 WARNING @ Thu, 09 Dec 2021 01:32:54: Fewer paired peaks (965) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 965 pairs to build model! INFO @ Thu, 09 Dec 2021 01:32:54: start model_add_line... INFO @ Thu, 09 Dec 2021 01:32:54: start X-correlation... INFO @ Thu, 09 Dec 2021 01:32:54: end of X-cor INFO @ Thu, 09 Dec 2021 01:32:54: #2 finished! INFO @ Thu, 09 Dec 2021 01:32:54: #2 predicted fragment length is 232 bps INFO @ Thu, 09 Dec 2021 01:32:54: #2 alternative fragment length(s) may be 232 bps INFO @ Thu, 09 Dec 2021 01:32:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.05_model.r WARNING @ Thu, 09 Dec 2021 01:32:54: #2 Since the d (232) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:32:54: #2 You may need to consider one of the other alternative d(s): 232 WARNING @ Thu, 09 Dec 2021 01:32:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 01:32:54: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:32:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:32:55: 17000000 INFO @ Thu, 09 Dec 2021 01:32:59: 23000000 INFO @ Thu, 09 Dec 2021 01:33:00: 18000000 INFO @ Thu, 09 Dec 2021 01:33:05: 24000000 INFO @ Thu, 09 Dec 2021 01:33:06: 19000000 INFO @ Thu, 09 Dec 2021 01:33:10: 25000000 INFO @ Thu, 09 Dec 2021 01:33:12: 20000000 INFO @ Thu, 09 Dec 2021 01:33:13: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:33:16: 26000000 INFO @ Thu, 09 Dec 2021 01:33:17: 21000000 INFO @ Thu, 09 Dec 2021 01:33:21: 27000000 INFO @ Thu, 09 Dec 2021 01:33:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.05_peaks.xls INFO @ Thu, 09 Dec 2021 01:33:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:33:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.05_summits.bed INFO @ Thu, 09 Dec 2021 01:33:22: 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 (6973 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:33:23: 22000000 INFO @ Thu, 09 Dec 2021 01:33:27: 28000000 INFO @ Thu, 09 Dec 2021 01:33:28: 23000000 INFO @ Thu, 09 Dec 2021 01:33:29: #1 tag size is determined as 125 bps INFO @ Thu, 09 Dec 2021 01:33:29: #1 tag size = 125 INFO @ Thu, 09 Dec 2021 01:33:29: #1 total tags in treatment: 11893730 INFO @ Thu, 09 Dec 2021 01:33:29: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:33:29: #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 01:33:30: #1 tags after filtering in treatment: 8227587 INFO @ Thu, 09 Dec 2021 01:33:30: #1 Redundant rate of treatment: 0.31 INFO @ Thu, 09 Dec 2021 01:33:30: #1 finished! INFO @ Thu, 09 Dec 2021 01:33:30: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:33:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:33:30: #2 number of paired peaks: 965 WARNING @ Thu, 09 Dec 2021 01:33:30: Fewer paired peaks (965) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 965 pairs to build model! INFO @ Thu, 09 Dec 2021 01:33:30: start model_add_line... INFO @ Thu, 09 Dec 2021 01:33:30: start X-correlation... INFO @ Thu, 09 Dec 2021 01:33:30: end of X-cor INFO @ Thu, 09 Dec 2021 01:33:30: #2 finished! INFO @ Thu, 09 Dec 2021 01:33:30: #2 predicted fragment length is 232 bps INFO @ Thu, 09 Dec 2021 01:33:30: #2 alternative fragment length(s) may be 232 bps INFO @ Thu, 09 Dec 2021 01:33:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.10_model.r WARNING @ Thu, 09 Dec 2021 01:33:30: #2 Since the d (232) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:33:30: #2 You may need to consider one of the other alternative d(s): 232 WARNING @ Thu, 09 Dec 2021 01:33:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 01:33:30: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:33:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:33:34: 24000000 INFO @ Thu, 09 Dec 2021 01:33:39: 25000000 INFO @ Thu, 09 Dec 2021 01:33:45: 26000000 INFO @ Thu, 09 Dec 2021 01:33:49: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:33:50: 27000000 INFO @ Thu, 09 Dec 2021 01:33:55: 28000000 INFO @ Thu, 09 Dec 2021 01:33:58: #1 tag size is determined as 125 bps INFO @ Thu, 09 Dec 2021 01:33:58: #1 tag size = 125 INFO @ Thu, 09 Dec 2021 01:33:58: #1 total tags in treatment: 11893730 INFO @ Thu, 09 Dec 2021 01:33:58: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:33:58: #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 01:33:58: #1 tags after filtering in treatment: 8227587 INFO @ Thu, 09 Dec 2021 01:33:58: #1 Redundant rate of treatment: 0.31 INFO @ Thu, 09 Dec 2021 01:33:58: #1 finished! INFO @ Thu, 09 Dec 2021 01:33:58: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:33:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:33:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.10_peaks.xls INFO @ Thu, 09 Dec 2021 01:33:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:33:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.10_summits.bed INFO @ Thu, 09 Dec 2021 01:33:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4232 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:33:58: #2 number of paired peaks: 965 WARNING @ Thu, 09 Dec 2021 01:33:58: Fewer paired peaks (965) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 965 pairs to build model! INFO @ Thu, 09 Dec 2021 01:33:58: start model_add_line... INFO @ Thu, 09 Dec 2021 01:33:58: start X-correlation... INFO @ Thu, 09 Dec 2021 01:33:59: end of X-cor INFO @ Thu, 09 Dec 2021 01:33:59: #2 finished! INFO @ Thu, 09 Dec 2021 01:33:59: #2 predicted fragment length is 232 bps INFO @ Thu, 09 Dec 2021 01:33:59: #2 alternative fragment length(s) may be 232 bps INFO @ Thu, 09 Dec 2021 01:33:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.20_model.r WARNING @ Thu, 09 Dec 2021 01:33:59: #2 Since the d (232) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:33:59: #2 You may need to consider one of the other alternative d(s): 232 WARNING @ Thu, 09 Dec 2021 01:33:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 01:33:59: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:33:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 01:34:17: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:34:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.20_peaks.xls INFO @ Thu, 09 Dec 2021 01:34:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:34:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845643/SRX8845643.20_summits.bed INFO @ Thu, 09 Dec 2021 01:34:26: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1894 records, 4 fields): 4 millis CompletedMACS2peakCalling