Job ID = 12265398 SRX = SRX4029336 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: 00:19:59 24327078 reads; of these: 24327078 (100.00%) were paired; of these: 11783422 (48.44%) aligned concordantly 0 times 10064962 (41.37%) aligned concordantly exactly 1 time 2478694 (10.19%) aligned concordantly >1 times ---- 11783422 pairs aligned concordantly 0 times; of these: 1913518 (16.24%) aligned discordantly 1 time ---- 9869904 pairs aligned 0 times concordantly or discordantly; of these: 19739808 mates make up the pairs; of these: 17789230 (90.12%) aligned 0 times 855358 (4.33%) aligned exactly 1 time 1095220 (5.55%) aligned >1 times 63.44% overall alignment rate Time searching: 00:20:00 Overall time: 00:20:00 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 16 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] 7932718 / 14364633 = 0.5522 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 07:17:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.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 07:17:20: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:17:20: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:17:26: 1000000 INFO @ Sat, 03 Apr 2021 07:17:31: 2000000 INFO @ Sat, 03 Apr 2021 07:17:36: 3000000 INFO @ Sat, 03 Apr 2021 07:17:42: 4000000 INFO @ Sat, 03 Apr 2021 07:17:47: 5000000 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 07:17:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.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 07:17:50: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:17:50: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:17:53: 6000000 INFO @ Sat, 03 Apr 2021 07:17:57: 1000000 INFO @ Sat, 03 Apr 2021 07:17:58: 7000000 INFO @ Sat, 03 Apr 2021 07:18:03: 2000000 INFO @ Sat, 03 Apr 2021 07:18:04: 8000000 INFO @ Sat, 03 Apr 2021 07:18:10: 3000000 INFO @ Sat, 03 Apr 2021 07:18:10: 9000000 INFO @ Sat, 03 Apr 2021 07:18:16: 4000000 INFO @ Sat, 03 Apr 2021 07:18:16: 10000000 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 07:18:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.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 07:18:20: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:18:20: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:18:22: 11000000 INFO @ Sat, 03 Apr 2021 07:18:22: 5000000 INFO @ Sat, 03 Apr 2021 07:18:27: 1000000 INFO @ Sat, 03 Apr 2021 07:18:28: 12000000 INFO @ Sat, 03 Apr 2021 07:18:29: 6000000 INFO @ Sat, 03 Apr 2021 07:18:33: 2000000 INFO @ Sat, 03 Apr 2021 07:18:33: 13000000 INFO @ Sat, 03 Apr 2021 07:18:35: 7000000 INFO @ Sat, 03 Apr 2021 07:18:39: 14000000 INFO @ Sat, 03 Apr 2021 07:18:40: 3000000 INFO @ Sat, 03 Apr 2021 07:18:42: 8000000 INFO @ Sat, 03 Apr 2021 07:18:45: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 07:18:45: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 07:18:45: #1 total tags in treatment: 5398154 INFO @ Sat, 03 Apr 2021 07:18:45: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:18:45: #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 07:18:45: #1 tags after filtering in treatment: 3328748 INFO @ Sat, 03 Apr 2021 07:18:45: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 03 Apr 2021 07:18:45: #1 finished! INFO @ Sat, 03 Apr 2021 07:18:45: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:18:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:18:45: #2 number of paired peaks: 3148 INFO @ Sat, 03 Apr 2021 07:18:45: start model_add_line... INFO @ Sat, 03 Apr 2021 07:18:45: start X-correlation... INFO @ Sat, 03 Apr 2021 07:18:45: end of X-cor INFO @ Sat, 03 Apr 2021 07:18:45: #2 finished! INFO @ Sat, 03 Apr 2021 07:18:45: #2 predicted fragment length is 118 bps INFO @ Sat, 03 Apr 2021 07:18:45: #2 alternative fragment length(s) may be 118 bps INFO @ Sat, 03 Apr 2021 07:18:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.05_model.r WARNING @ Sat, 03 Apr 2021 07:18:45: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:18:45: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Sat, 03 Apr 2021 07:18:45: #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 07:18:45: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:18:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:18:46: 4000000 INFO @ Sat, 03 Apr 2021 07:18:48: 9000000 INFO @ Sat, 03 Apr 2021 07:18:52: 5000000 INFO @ Sat, 03 Apr 2021 07:18:55: 10000000 INFO @ Sat, 03 Apr 2021 07:18:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:18:59: 6000000 INFO @ Sat, 03 Apr 2021 07:19:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:19:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:19:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.05_summits.bed INFO @ Sat, 03 Apr 2021 07:19:00: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5238 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:19:01: 11000000 INFO @ Sat, 03 Apr 2021 07:19:05: 7000000 INFO @ Sat, 03 Apr 2021 07:19:07: 12000000 INFO @ Sat, 03 Apr 2021 07:19:12: 8000000 INFO @ Sat, 03 Apr 2021 07:19:13: 13000000 INFO @ Sat, 03 Apr 2021 07:19:18: 9000000 INFO @ Sat, 03 Apr 2021 07:19:19: 14000000 INFO @ Sat, 03 Apr 2021 07:19:25: 10000000 INFO @ Sat, 03 Apr 2021 07:19:25: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 07:19:25: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 07:19:25: #1 total tags in treatment: 5398154 INFO @ Sat, 03 Apr 2021 07:19:25: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:19:25: #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 07:19:26: #1 tags after filtering in treatment: 3328748 INFO @ Sat, 03 Apr 2021 07:19:26: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 03 Apr 2021 07:19:26: #1 finished! INFO @ Sat, 03 Apr 2021 07:19:26: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:19:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:19:26: #2 number of paired peaks: 3148 INFO @ Sat, 03 Apr 2021 07:19:26: start model_add_line... INFO @ Sat, 03 Apr 2021 07:19:26: start X-correlation... INFO @ Sat, 03 Apr 2021 07:19:26: end of X-cor INFO @ Sat, 03 Apr 2021 07:19:26: #2 finished! INFO @ Sat, 03 Apr 2021 07:19:26: #2 predicted fragment length is 118 bps INFO @ Sat, 03 Apr 2021 07:19:26: #2 alternative fragment length(s) may be 118 bps INFO @ Sat, 03 Apr 2021 07:19:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.10_model.r WARNING @ Sat, 03 Apr 2021 07:19:26: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:19:26: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Sat, 03 Apr 2021 07:19:26: #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 07:19:26: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:19:26: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:19:31: 11000000 INFO @ Sat, 03 Apr 2021 07:19:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:19:37: 12000000 INFO @ Sat, 03 Apr 2021 07:19:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:19:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:19:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.10_summits.bed INFO @ Sat, 03 Apr 2021 07:19:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3113 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:19:43: 13000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:19:49: 14000000 INFO @ Sat, 03 Apr 2021 07:19:55: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 07:19:55: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 07:19:55: #1 total tags in treatment: 5398154 INFO @ Sat, 03 Apr 2021 07:19:55: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:19:55: #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 07:19:56: #1 tags after filtering in treatment: 3328748 INFO @ Sat, 03 Apr 2021 07:19:56: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 03 Apr 2021 07:19:56: #1 finished! INFO @ Sat, 03 Apr 2021 07:19:56: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:19:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:19:56: #2 number of paired peaks: 3148 INFO @ Sat, 03 Apr 2021 07:19:56: start model_add_line... INFO @ Sat, 03 Apr 2021 07:19:56: start X-correlation... INFO @ Sat, 03 Apr 2021 07:19:56: end of X-cor INFO @ Sat, 03 Apr 2021 07:19:56: #2 finished! INFO @ Sat, 03 Apr 2021 07:19:56: #2 predicted fragment length is 118 bps INFO @ Sat, 03 Apr 2021 07:19:56: #2 alternative fragment length(s) may be 118 bps INFO @ Sat, 03 Apr 2021 07:19:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.20_model.r WARNING @ Sat, 03 Apr 2021 07:19:56: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:19:56: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Sat, 03 Apr 2021 07:19:56: #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 07:19:56: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:19:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:20:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:20:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:20:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:20:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4029336/SRX4029336.20_summits.bed INFO @ Sat, 03 Apr 2021 07:20:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1411 records, 4 fields): 3 millis CompletedMACS2peakCalling