Job ID = 14158494 SRX = SRX9025734 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23004749 spots for SRR12551289/SRR12551289.sra Written 23004749 spots for SRR12551289/SRR12551289.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159224 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:30:00 23004749 reads; of these: 23004749 (100.00%) were paired; of these: 6458818 (28.08%) aligned concordantly 0 times 14182531 (61.65%) aligned concordantly exactly 1 time 2363400 (10.27%) aligned concordantly >1 times ---- 6458818 pairs aligned concordantly 0 times; of these: 2557540 (39.60%) aligned discordantly 1 time ---- 3901278 pairs aligned 0 times concordantly or discordantly; of these: 7802556 mates make up the pairs; of these: 6635536 (85.04%) aligned 0 times 535568 (6.86%) aligned exactly 1 time 631452 (8.09%) aligned >1 times 85.58% overall alignment rate Time searching: 00:30:01 Overall time: 00:30:01 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 20 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] 1275186 / 18900482 = 0.0675 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 18:26:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.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 18:26:56: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:26:56: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:27:05: 1000000 INFO @ Wed, 08 Dec 2021 18:27:14: 2000000 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 18:27:24: 3000000 INFO @ Wed, 08 Dec 2021 18:27:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.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 18:27:26: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:27:26: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:27:33: 4000000 INFO @ Wed, 08 Dec 2021 18:27:36: 1000000 INFO @ Wed, 08 Dec 2021 18:27:43: 5000000 INFO @ Wed, 08 Dec 2021 18:27:46: 2000000 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 18:27:54: 6000000 INFO @ Wed, 08 Dec 2021 18:27:56: 3000000 INFO @ Wed, 08 Dec 2021 18:27:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.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 18:27:56: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:27:56: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:28:04: 1000000 INFO @ Wed, 08 Dec 2021 18:28:04: 7000000 INFO @ Wed, 08 Dec 2021 18:28:06: 4000000 INFO @ Wed, 08 Dec 2021 18:28:11: 2000000 INFO @ Wed, 08 Dec 2021 18:28:15: 8000000 INFO @ Wed, 08 Dec 2021 18:28:17: 5000000 INFO @ Wed, 08 Dec 2021 18:28:19: 3000000 INFO @ Wed, 08 Dec 2021 18:28:26: 9000000 INFO @ Wed, 08 Dec 2021 18:28:26: 4000000 INFO @ Wed, 08 Dec 2021 18:28:28: 6000000 INFO @ Wed, 08 Dec 2021 18:28:34: 5000000 INFO @ Wed, 08 Dec 2021 18:28:36: 10000000 INFO @ Wed, 08 Dec 2021 18:28:38: 7000000 INFO @ Wed, 08 Dec 2021 18:28:41: 6000000 INFO @ Wed, 08 Dec 2021 18:28:47: 11000000 INFO @ Wed, 08 Dec 2021 18:28:49: 8000000 INFO @ Wed, 08 Dec 2021 18:28:49: 7000000 INFO @ Wed, 08 Dec 2021 18:28:56: 8000000 INFO @ Wed, 08 Dec 2021 18:28:57: 12000000 INFO @ Wed, 08 Dec 2021 18:28:59: 9000000 INFO @ Wed, 08 Dec 2021 18:29:04: 9000000 INFO @ Wed, 08 Dec 2021 18:29:07: 13000000 INFO @ Wed, 08 Dec 2021 18:29:09: 10000000 INFO @ Wed, 08 Dec 2021 18:29:13: 10000000 INFO @ Wed, 08 Dec 2021 18:29:17: 14000000 INFO @ Wed, 08 Dec 2021 18:29:19: 11000000 INFO @ Wed, 08 Dec 2021 18:29:22: 11000000 INFO @ Wed, 08 Dec 2021 18:29:27: 15000000 INFO @ Wed, 08 Dec 2021 18:29:29: 12000000 INFO @ Wed, 08 Dec 2021 18:29:29: 12000000 INFO @ Wed, 08 Dec 2021 18:29:37: 16000000 INFO @ Wed, 08 Dec 2021 18:29:37: 13000000 INFO @ Wed, 08 Dec 2021 18:29:38: 13000000 INFO @ Wed, 08 Dec 2021 18:29:45: 14000000 INFO @ Wed, 08 Dec 2021 18:29:47: 17000000 INFO @ Wed, 08 Dec 2021 18:29:47: 14000000 INFO @ Wed, 08 Dec 2021 18:29:54: 15000000 INFO @ Wed, 08 Dec 2021 18:29:56: 15000000 INFO @ Wed, 08 Dec 2021 18:29:57: 18000000 INFO @ Wed, 08 Dec 2021 18:30:02: 16000000 INFO @ Wed, 08 Dec 2021 18:30:05: 16000000 INFO @ Wed, 08 Dec 2021 18:30:06: 19000000 INFO @ Wed, 08 Dec 2021 18:30:11: 17000000 INFO @ Wed, 08 Dec 2021 18:30:13: 17000000 INFO @ Wed, 08 Dec 2021 18:30:14: 20000000 INFO @ Wed, 08 Dec 2021 18:30:19: 18000000 INFO @ Wed, 08 Dec 2021 18:30:23: 18000000 INFO @ Wed, 08 Dec 2021 18:30:23: 21000000 INFO @ Wed, 08 Dec 2021 18:30:27: 19000000 INFO @ Wed, 08 Dec 2021 18:30:32: 22000000 INFO @ Wed, 08 Dec 2021 18:30:32: 19000000 INFO @ Wed, 08 Dec 2021 18:30:35: 20000000 INFO @ Wed, 08 Dec 2021 18:30:41: 23000000 INFO @ Wed, 08 Dec 2021 18:30:42: 20000000 INFO @ Wed, 08 Dec 2021 18:30:43: 21000000 INFO @ Wed, 08 Dec 2021 18:30:50: 22000000 INFO @ Wed, 08 Dec 2021 18:30:51: 24000000 INFO @ Wed, 08 Dec 2021 18:30:52: 21000000 INFO @ Wed, 08 Dec 2021 18:30:58: 23000000 INFO @ Wed, 08 Dec 2021 18:31:00: 25000000 INFO @ Wed, 08 Dec 2021 18:31:02: 22000000 INFO @ Wed, 08 Dec 2021 18:31:05: 24000000 INFO @ Wed, 08 Dec 2021 18:31:09: 26000000 INFO @ Wed, 08 Dec 2021 18:31:12: 23000000 INFO @ Wed, 08 Dec 2021 18:31:12: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:31:18: 27000000 INFO @ Wed, 08 Dec 2021 18:31:20: 26000000 INFO @ Wed, 08 Dec 2021 18:31:22: 24000000 INFO @ Wed, 08 Dec 2021 18:31:27: 28000000 INFO @ Wed, 08 Dec 2021 18:31:28: 27000000 INFO @ Wed, 08 Dec 2021 18:31:31: 25000000 INFO @ Wed, 08 Dec 2021 18:31:36: 29000000 INFO @ Wed, 08 Dec 2021 18:31:37: 28000000 INFO @ Wed, 08 Dec 2021 18:31:40: 26000000 INFO @ Wed, 08 Dec 2021 18:31:45: 29000000 INFO @ Wed, 08 Dec 2021 18:31:45: 30000000 INFO @ Wed, 08 Dec 2021 18:31:49: 27000000 INFO @ Wed, 08 Dec 2021 18:31:54: 30000000 INFO @ Wed, 08 Dec 2021 18:31:55: 31000000 INFO @ Wed, 08 Dec 2021 18:31:59: 28000000 INFO @ Wed, 08 Dec 2021 18:32:02: 31000000 INFO @ Wed, 08 Dec 2021 18:32:05: 32000000 INFO @ Wed, 08 Dec 2021 18:32:07: 29000000 INFO @ Wed, 08 Dec 2021 18:32:09: 32000000 INFO @ Wed, 08 Dec 2021 18:32:14: 33000000 INFO @ Wed, 08 Dec 2021 18:32:16: 30000000 INFO @ Wed, 08 Dec 2021 18:32:16: 33000000 INFO @ Wed, 08 Dec 2021 18:32:23: 34000000 INFO @ Wed, 08 Dec 2021 18:32:24: 34000000 INFO @ Wed, 08 Dec 2021 18:32:25: 31000000 INFO @ Wed, 08 Dec 2021 18:32:31: 35000000 INFO @ Wed, 08 Dec 2021 18:32:32: 35000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:32:34: 32000000 INFO @ Wed, 08 Dec 2021 18:32:39: 36000000 INFO @ Wed, 08 Dec 2021 18:32:41: 36000000 INFO @ Wed, 08 Dec 2021 18:32:44: 33000000 INFO @ Wed, 08 Dec 2021 18:32:45: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 18:32:45: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 18:32:45: #1 total tags in treatment: 15446920 INFO @ Wed, 08 Dec 2021 18:32:45: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:32:45: #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 18:32:45: #1 tags after filtering in treatment: 12087915 INFO @ Wed, 08 Dec 2021 18:32:45: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 08 Dec 2021 18:32:45: #1 finished! INFO @ Wed, 08 Dec 2021 18:32:45: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:32:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:32:46: #2 number of paired peaks: 117 WARNING @ Wed, 08 Dec 2021 18:32:46: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Wed, 08 Dec 2021 18:32:46: start model_add_line... INFO @ Wed, 08 Dec 2021 18:32:46: start X-correlation... INFO @ Wed, 08 Dec 2021 18:32:46: end of X-cor INFO @ Wed, 08 Dec 2021 18:32:46: #2 finished! INFO @ Wed, 08 Dec 2021 18:32:46: #2 predicted fragment length is 96 bps INFO @ Wed, 08 Dec 2021 18:32:46: #2 alternative fragment length(s) may be 12,17,64,70,96,182,212,238,265,270,323,498,524,558,563 bps INFO @ Wed, 08 Dec 2021 18:32:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.20_model.r WARNING @ Wed, 08 Dec 2021 18:32:46: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:32:46: #2 You may need to consider one of the other alternative d(s): 12,17,64,70,96,182,212,238,265,270,323,498,524,558,563 WARNING @ Wed, 08 Dec 2021 18:32:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 18:32:46: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:32:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:32:48: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 18:32:48: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 18:32:48: #1 total tags in treatment: 15446920 INFO @ Wed, 08 Dec 2021 18:32:48: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:32:48: #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 18:32:48: #1 tags after filtering in treatment: 12087915 INFO @ Wed, 08 Dec 2021 18:32:48: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 08 Dec 2021 18:32:48: #1 finished! INFO @ Wed, 08 Dec 2021 18:32:48: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:32:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:32:49: #2 number of paired peaks: 117 WARNING @ Wed, 08 Dec 2021 18:32:49: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Wed, 08 Dec 2021 18:32:49: start model_add_line... INFO @ Wed, 08 Dec 2021 18:32:49: start X-correlation... INFO @ Wed, 08 Dec 2021 18:32:49: end of X-cor INFO @ Wed, 08 Dec 2021 18:32:49: #2 finished! INFO @ Wed, 08 Dec 2021 18:32:49: #2 predicted fragment length is 96 bps INFO @ Wed, 08 Dec 2021 18:32:49: #2 alternative fragment length(s) may be 12,17,64,70,96,182,212,238,265,270,323,498,524,558,563 bps INFO @ Wed, 08 Dec 2021 18:32:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.05_model.r WARNING @ Wed, 08 Dec 2021 18:32:49: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:32:49: #2 You may need to consider one of the other alternative d(s): 12,17,64,70,96,182,212,238,265,270,323,498,524,558,563 WARNING @ Wed, 08 Dec 2021 18:32:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 18:32:49: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:32:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:32:54: 34000000 INFO @ Wed, 08 Dec 2021 18:33:03: 35000000 INFO @ Wed, 08 Dec 2021 18:33:06: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:33:10: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:33:13: 36000000 INFO @ Wed, 08 Dec 2021 18:33:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:33:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:33:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.20_summits.bed INFO @ Wed, 08 Dec 2021 18:33:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (84 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:33:20: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 18:33:20: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 18:33:20: #1 total tags in treatment: 15446920 INFO @ Wed, 08 Dec 2021 18:33:20: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:33:20: #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 18:33:20: #1 tags after filtering in treatment: 12087915 INFO @ Wed, 08 Dec 2021 18:33:20: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 08 Dec 2021 18:33:20: #1 finished! INFO @ Wed, 08 Dec 2021 18:33:20: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:33:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:33:21: #2 number of paired peaks: 117 WARNING @ Wed, 08 Dec 2021 18:33:21: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Wed, 08 Dec 2021 18:33:21: start model_add_line... INFO @ Wed, 08 Dec 2021 18:33:21: start X-correlation... INFO @ Wed, 08 Dec 2021 18:33:21: end of X-cor INFO @ Wed, 08 Dec 2021 18:33:21: #2 finished! INFO @ Wed, 08 Dec 2021 18:33:21: #2 predicted fragment length is 96 bps INFO @ Wed, 08 Dec 2021 18:33:21: #2 alternative fragment length(s) may be 12,17,64,70,96,182,212,238,265,270,323,498,524,558,563 bps INFO @ Wed, 08 Dec 2021 18:33:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.10_model.r WARNING @ Wed, 08 Dec 2021 18:33:21: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:33:21: #2 You may need to consider one of the other alternative d(s): 12,17,64,70,96,182,212,238,265,270,323,498,524,558,563 WARNING @ Wed, 08 Dec 2021 18:33:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 18:33:21: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:33:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:33:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:33:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:33:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.05_summits.bed INFO @ Wed, 08 Dec 2021 18:33:22: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (325 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:33:42: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:33:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:33:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:33:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9025734/SRX9025734.10_summits.bed INFO @ Wed, 08 Dec 2021 18:33:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (188 records, 4 fields): 16 millis CompletedMACS2peakCalling