Job ID = 12265275 SRX = SRX3029121 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: 00:18:00 15580944 reads; of these: 15580944 (100.00%) were paired; of these: 4737464 (30.41%) aligned concordantly 0 times 9454767 (60.68%) aligned concordantly exactly 1 time 1388713 (8.91%) aligned concordantly >1 times ---- 4737464 pairs aligned concordantly 0 times; of these: 1381029 (29.15%) aligned discordantly 1 time ---- 3356435 pairs aligned 0 times concordantly or discordantly; of these: 6712870 mates make up the pairs; of these: 5990064 (89.23%) aligned 0 times 326472 (4.86%) aligned exactly 1 time 396334 (5.90%) aligned >1 times 80.78% overall alignment rate Time searching: 00:18:00 Overall time: 00:18:00 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] 2752285 / 12118239 = 0.2271 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:51:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.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 @ Sat, 03 Apr 2021 06:51:53: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:51:53: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:52:01: 1000000 INFO @ Sat, 03 Apr 2021 06:52:09: 2000000 INFO @ Sat, 03 Apr 2021 06:52:17: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:52:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.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 @ Sat, 03 Apr 2021 06:52:23: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:52:23: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:52:25: 4000000 INFO @ Sat, 03 Apr 2021 06:52:33: 1000000 INFO @ Sat, 03 Apr 2021 06:52:34: 5000000 INFO @ Sat, 03 Apr 2021 06:52:42: 2000000 INFO @ Sat, 03 Apr 2021 06:52:43: 6000000 INFO @ Sat, 03 Apr 2021 06:52:51: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:52:52: 7000000 INFO @ Sat, 03 Apr 2021 06:52:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.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 @ Sat, 03 Apr 2021 06:52:53: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:52:53: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:53:00: 4000000 INFO @ Sat, 03 Apr 2021 06:53:01: 8000000 INFO @ Sat, 03 Apr 2021 06:53:02: 1000000 INFO @ Sat, 03 Apr 2021 06:53:10: 5000000 INFO @ Sat, 03 Apr 2021 06:53:10: 2000000 INFO @ Sat, 03 Apr 2021 06:53:11: 9000000 INFO @ Sat, 03 Apr 2021 06:53:18: 3000000 INFO @ Sat, 03 Apr 2021 06:53:19: 6000000 INFO @ Sat, 03 Apr 2021 06:53:21: 10000000 INFO @ Sat, 03 Apr 2021 06:53:27: 4000000 INFO @ Sat, 03 Apr 2021 06:53:28: 7000000 INFO @ Sat, 03 Apr 2021 06:53:30: 11000000 INFO @ Sat, 03 Apr 2021 06:53:35: 5000000 INFO @ Sat, 03 Apr 2021 06:53:38: 8000000 INFO @ Sat, 03 Apr 2021 06:53:40: 12000000 INFO @ Sat, 03 Apr 2021 06:53:43: 6000000 INFO @ Sat, 03 Apr 2021 06:53:47: 9000000 INFO @ Sat, 03 Apr 2021 06:53:49: 13000000 INFO @ Sat, 03 Apr 2021 06:53:52: 7000000 INFO @ Sat, 03 Apr 2021 06:53:56: 10000000 INFO @ Sat, 03 Apr 2021 06:53:58: 14000000 INFO @ Sat, 03 Apr 2021 06:54:00: 8000000 INFO @ Sat, 03 Apr 2021 06:54:06: 11000000 INFO @ Sat, 03 Apr 2021 06:54:08: 15000000 INFO @ Sat, 03 Apr 2021 06:54:08: 9000000 INFO @ Sat, 03 Apr 2021 06:54:15: 12000000 INFO @ Sat, 03 Apr 2021 06:54:17: 10000000 INFO @ Sat, 03 Apr 2021 06:54:17: 16000000 INFO @ Sat, 03 Apr 2021 06:54:24: 13000000 INFO @ Sat, 03 Apr 2021 06:54:25: 11000000 INFO @ Sat, 03 Apr 2021 06:54:26: 17000000 INFO @ Sat, 03 Apr 2021 06:54:33: 12000000 INFO @ Sat, 03 Apr 2021 06:54:33: 14000000 INFO @ Sat, 03 Apr 2021 06:54:35: 18000000 INFO @ Sat, 03 Apr 2021 06:54:41: 13000000 INFO @ Sat, 03 Apr 2021 06:54:42: 15000000 INFO @ Sat, 03 Apr 2021 06:54:44: 19000000 INFO @ Sat, 03 Apr 2021 06:54:49: 14000000 INFO @ Sat, 03 Apr 2021 06:54:49: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:54:49: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:54:49: #1 total tags in treatment: 8387720 INFO @ Sat, 03 Apr 2021 06:54:49: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:54:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:54:49: #1 tags after filtering in treatment: 5895876 INFO @ Sat, 03 Apr 2021 06:54:49: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 06:54:49: #1 finished! INFO @ Sat, 03 Apr 2021 06:54:49: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:54:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:54:50: #2 number of paired peaks: 1253 INFO @ Sat, 03 Apr 2021 06:54:50: start model_add_line... INFO @ Sat, 03 Apr 2021 06:54:50: start X-correlation... INFO @ Sat, 03 Apr 2021 06:54:50: end of X-cor INFO @ Sat, 03 Apr 2021 06:54:50: #2 finished! INFO @ Sat, 03 Apr 2021 06:54:50: #2 predicted fragment length is 119 bps INFO @ Sat, 03 Apr 2021 06:54:50: #2 alternative fragment length(s) may be 119 bps INFO @ Sat, 03 Apr 2021 06:54:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.05_model.r WARNING @ Sat, 03 Apr 2021 06:54:50: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:54:50: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Sat, 03 Apr 2021 06:54:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:54:50: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:54:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:54:51: 16000000 INFO @ Sat, 03 Apr 2021 06:54:57: 15000000 INFO @ Sat, 03 Apr 2021 06:54:58: 17000000 INFO @ Sat, 03 Apr 2021 06:55:05: 16000000 INFO @ Sat, 03 Apr 2021 06:55:06: 18000000 INFO @ Sat, 03 Apr 2021 06:55:09: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:55:12: 17000000 INFO @ Sat, 03 Apr 2021 06:55:14: 19000000 INFO @ Sat, 03 Apr 2021 06:55:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:55:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:55:19: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:55:19: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:55:19: #1 total tags in treatment: 8387720 INFO @ Sat, 03 Apr 2021 06:55:19: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:55:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:55:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.05_summits.bed INFO @ Sat, 03 Apr 2021 06:55:19: Done! INFO @ Sat, 03 Apr 2021 06:55:19: #1 tags after filtering in treatment: 5895876 INFO @ Sat, 03 Apr 2021 06:55:19: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 06:55:19: #1 finished! INFO @ Sat, 03 Apr 2021 06:55:19: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:55:19: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (6692 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:55:20: #2 number of paired peaks: 1253 INFO @ Sat, 03 Apr 2021 06:55:20: start model_add_line... INFO @ Sat, 03 Apr 2021 06:55:20: start X-correlation... INFO @ Sat, 03 Apr 2021 06:55:20: end of X-cor INFO @ Sat, 03 Apr 2021 06:55:20: #2 finished! INFO @ Sat, 03 Apr 2021 06:55:20: #2 predicted fragment length is 119 bps INFO @ Sat, 03 Apr 2021 06:55:20: #2 alternative fragment length(s) may be 119 bps INFO @ Sat, 03 Apr 2021 06:55:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.10_model.r WARNING @ Sat, 03 Apr 2021 06:55:20: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:55:20: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Sat, 03 Apr 2021 06:55:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:55:20: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:55:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:55:20: 18000000 INFO @ Sat, 03 Apr 2021 06:55:27: 19000000 INFO @ Sat, 03 Apr 2021 06:55:32: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:55:32: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:55:32: #1 total tags in treatment: 8387720 INFO @ Sat, 03 Apr 2021 06:55:32: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:55:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:55:32: #1 tags after filtering in treatment: 5895876 INFO @ Sat, 03 Apr 2021 06:55:32: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 06:55:32: #1 finished! INFO @ Sat, 03 Apr 2021 06:55:32: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:55:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:55:33: #2 number of paired peaks: 1253 INFO @ Sat, 03 Apr 2021 06:55:33: start model_add_line... INFO @ Sat, 03 Apr 2021 06:55:33: start X-correlation... INFO @ Sat, 03 Apr 2021 06:55:33: end of X-cor INFO @ Sat, 03 Apr 2021 06:55:33: #2 finished! INFO @ Sat, 03 Apr 2021 06:55:33: #2 predicted fragment length is 119 bps INFO @ Sat, 03 Apr 2021 06:55:33: #2 alternative fragment length(s) may be 119 bps INFO @ Sat, 03 Apr 2021 06:55:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.20_model.r WARNING @ Sat, 03 Apr 2021 06:55:33: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:55:33: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Sat, 03 Apr 2021 06:55:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:55:33: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:55:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:55:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:55:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:55:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:55:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.10_summits.bed INFO @ Sat, 03 Apr 2021 06:55:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4159 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:55:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:56:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:56:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:56:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3029121/SRX3029121.20_summits.bed INFO @ Sat, 03 Apr 2021 06:56:00: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2097 records, 4 fields): 7 millis CompletedMACS2peakCalling