Job ID = 12264756 SRX = SRX3029121 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15580944 spots for SRR5860421/SRR5860421.sra Written 15580944 spots for SRR5860421/SRR5860421.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265275 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:17:22 15580944 reads; of these: 15580944 (100.00%) were paired; of these: 4737643 (30.41%) aligned concordantly 0 times 9454651 (60.68%) aligned concordantly exactly 1 time 1388650 (8.91%) aligned concordantly >1 times ---- 4737643 pairs aligned concordantly 0 times; of these: 1380517 (29.14%) aligned discordantly 1 time ---- 3357126 pairs aligned 0 times concordantly or discordantly; of these: 6714252 mates make up the pairs; of these: 5991416 (89.23%) aligned 0 times 326506 (4.86%) aligned exactly 1 time 396330 (5.90%) aligned >1 times 80.77% overall alignment rate Time searching: 00:17:22 Overall time: 00:17:22 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] 2752124 / 12117549 = 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 06:22:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3029121/SRX3029121.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3029121/SRX3029121.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3029121/SRX3029121.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 06:22:34: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:22:34: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:22:39: 1000000 INFO @ Sat, 03 Apr 2021 06:22:44: 2000000 INFO @ Sat, 03 Apr 2021 06:22:49: 3000000 INFO @ Sat, 03 Apr 2021 06:22:55: 4000000 INFO @ Sat, 03 Apr 2021 06:23:00: 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 06:23:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3029121/SRX3029121.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3029121/SRX3029121.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3029121/SRX3029121.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 06:23:02: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:23:02: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:23:05: 6000000 INFO @ Sat, 03 Apr 2021 06:23:08: 1000000 INFO @ Sat, 03 Apr 2021 06:23:11: 7000000 INFO @ Sat, 03 Apr 2021 06:23:14: 2000000 INFO @ Sat, 03 Apr 2021 06:23:17: 8000000 INFO @ Sat, 03 Apr 2021 06:23:20: 3000000 INFO @ Sat, 03 Apr 2021 06:23:22: 9000000 INFO @ Sat, 03 Apr 2021 06:23:25: 4000000 INFO @ Sat, 03 Apr 2021 06:23:28: 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 06:23:31: 5000000 INFO @ Sat, 03 Apr 2021 06:23:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3029121/SRX3029121.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3029121/SRX3029121.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3029121/SRX3029121.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 06:23:33: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:23:33: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:23:34: 11000000 INFO @ Sat, 03 Apr 2021 06:23:37: 6000000 INFO @ Sat, 03 Apr 2021 06:23:39: 1000000 INFO @ Sat, 03 Apr 2021 06:23:40: 12000000 INFO @ Sat, 03 Apr 2021 06:23:44: 7000000 INFO @ Sat, 03 Apr 2021 06:23:46: 2000000 INFO @ Sat, 03 Apr 2021 06:23:47: 13000000 INFO @ Sat, 03 Apr 2021 06:23:51: 8000000 INFO @ Sat, 03 Apr 2021 06:23:52: 3000000 INFO @ Sat, 03 Apr 2021 06:23:54: 14000000 INFO @ Sat, 03 Apr 2021 06:23:57: 9000000 INFO @ Sat, 03 Apr 2021 06:23:59: 4000000 INFO @ Sat, 03 Apr 2021 06:24:00: 15000000 INFO @ Sat, 03 Apr 2021 06:24:04: 10000000 INFO @ Sat, 03 Apr 2021 06:24:05: 5000000 INFO @ Sat, 03 Apr 2021 06:24:06: 16000000 INFO @ Sat, 03 Apr 2021 06:24:10: 11000000 INFO @ Sat, 03 Apr 2021 06:24:12: 6000000 INFO @ Sat, 03 Apr 2021 06:24:13: 17000000 INFO @ Sat, 03 Apr 2021 06:24:17: 12000000 INFO @ Sat, 03 Apr 2021 06:24:18: 7000000 INFO @ Sat, 03 Apr 2021 06:24:19: 18000000 INFO @ Sat, 03 Apr 2021 06:24:23: 13000000 INFO @ Sat, 03 Apr 2021 06:24:25: 8000000 INFO @ Sat, 03 Apr 2021 06:24:25: 19000000 INFO @ Sat, 03 Apr 2021 06:24:29: 14000000 INFO @ Sat, 03 Apr 2021 06:24:29: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:24:29: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:24:29: #1 total tags in treatment: 8387576 INFO @ Sat, 03 Apr 2021 06:24:29: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:24:29: #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 06:24:30: #1 tags after filtering in treatment: 5895787 INFO @ Sat, 03 Apr 2021 06:24:30: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 06:24:30: #1 finished! INFO @ Sat, 03 Apr 2021 06:24:30: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:24:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:24:30: #2 number of paired peaks: 1250 INFO @ Sat, 03 Apr 2021 06:24:30: start model_add_line... INFO @ Sat, 03 Apr 2021 06:24:30: start X-correlation... INFO @ Sat, 03 Apr 2021 06:24:30: end of X-cor INFO @ Sat, 03 Apr 2021 06:24:30: #2 finished! INFO @ Sat, 03 Apr 2021 06:24:30: #2 predicted fragment length is 119 bps INFO @ Sat, 03 Apr 2021 06:24:30: #2 alternative fragment length(s) may be 119 bps INFO @ Sat, 03 Apr 2021 06:24:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3029121/SRX3029121.05_model.r WARNING @ Sat, 03 Apr 2021 06:24:30: #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 06:24:30: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Sat, 03 Apr 2021 06:24:30: #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 06:24:30: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:24:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:24:31: 9000000 INFO @ Sat, 03 Apr 2021 06:24:35: 15000000 INFO @ Sat, 03 Apr 2021 06:24:37: 10000000 INFO @ Sat, 03 Apr 2021 06:24:41: 16000000 INFO @ Sat, 03 Apr 2021 06:24:43: 11000000 INFO @ Sat, 03 Apr 2021 06:24:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:24:47: 17000000 INFO @ Sat, 03 Apr 2021 06:24:48: 12000000 INFO @ Sat, 03 Apr 2021 06:24:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3029121/SRX3029121.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:24:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3029121/SRX3029121.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:24:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3029121/SRX3029121.05_summits.bed INFO @ Sat, 03 Apr 2021 06:24:50: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6691 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:24:52: 18000000 INFO @ Sat, 03 Apr 2021 06:24:54: 13000000 INFO @ Sat, 03 Apr 2021 06:24:58: 19000000 INFO @ Sat, 03 Apr 2021 06:25:00: 14000000 INFO @ Sat, 03 Apr 2021 06:25:01: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:25:01: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:25:01: #1 total tags in treatment: 8387576 INFO @ Sat, 03 Apr 2021 06:25:01: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:25:01: #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 06:25:01: #1 tags after filtering in treatment: 5895787 INFO @ Sat, 03 Apr 2021 06:25:01: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 06:25:01: #1 finished! INFO @ Sat, 03 Apr 2021 06:25:01: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:25:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:25:02: #2 number of paired peaks: 1250 INFO @ Sat, 03 Apr 2021 06:25:02: start model_add_line... INFO @ Sat, 03 Apr 2021 06:25:02: start X-correlation... INFO @ Sat, 03 Apr 2021 06:25:02: end of X-cor INFO @ Sat, 03 Apr 2021 06:25:02: #2 finished! INFO @ Sat, 03 Apr 2021 06:25:02: #2 predicted fragment length is 119 bps INFO @ Sat, 03 Apr 2021 06:25:02: #2 alternative fragment length(s) may be 119 bps INFO @ Sat, 03 Apr 2021 06:25:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3029121/SRX3029121.10_model.r WARNING @ Sat, 03 Apr 2021 06:25:02: #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 06:25:02: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Sat, 03 Apr 2021 06:25:02: #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 06:25:02: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:25:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:25:05: 15000000 INFO @ Sat, 03 Apr 2021 06:25:10: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:25:15: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:25:15: 17000000 INFO @ Sat, 03 Apr 2021 06:25:21: 18000000 INFO @ Sat, 03 Apr 2021 06:25:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3029121/SRX3029121.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:25:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3029121/SRX3029121.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:25:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3029121/SRX3029121.10_summits.bed INFO @ Sat, 03 Apr 2021 06:25:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4160 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:25:26: 19000000 INFO @ Sat, 03 Apr 2021 06:25:30: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:25:30: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:25:30: #1 total tags in treatment: 8387576 INFO @ Sat, 03 Apr 2021 06:25:30: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:25:30: #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 06:25:30: #1 tags after filtering in treatment: 5895787 INFO @ Sat, 03 Apr 2021 06:25:30: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 06:25:30: #1 finished! INFO @ Sat, 03 Apr 2021 06:25:30: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:25:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:25:30: #2 number of paired peaks: 1250 INFO @ Sat, 03 Apr 2021 06:25:30: start model_add_line... INFO @ Sat, 03 Apr 2021 06:25:30: start X-correlation... INFO @ Sat, 03 Apr 2021 06:25:31: end of X-cor INFO @ Sat, 03 Apr 2021 06:25:31: #2 finished! INFO @ Sat, 03 Apr 2021 06:25:31: #2 predicted fragment length is 119 bps INFO @ Sat, 03 Apr 2021 06:25:31: #2 alternative fragment length(s) may be 119 bps INFO @ Sat, 03 Apr 2021 06:25:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3029121/SRX3029121.20_model.r WARNING @ Sat, 03 Apr 2021 06:25:31: #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 06:25:31: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Sat, 03 Apr 2021 06:25:31: #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 06:25:31: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:25:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:25:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:25:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3029121/SRX3029121.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:25:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3029121/SRX3029121.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:25:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3029121/SRX3029121.20_summits.bed INFO @ Sat, 03 Apr 2021 06:25:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (2097 records, 4 fields): 11 millis CompletedMACS2peakCalling