Job ID = 14159224 SRX = SRX9025734 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: 00:00:03 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:04 Multiseed full-index search: 00:27:47 23004749 reads; of these: 23004749 (100.00%) were paired; of these: 6458737 (28.08%) aligned concordantly 0 times 14182512 (61.65%) aligned concordantly exactly 1 time 2363500 (10.27%) aligned concordantly >1 times ---- 6458737 pairs aligned concordantly 0 times; of these: 2557971 (39.60%) aligned discordantly 1 time ---- 3900766 pairs aligned 0 times concordantly or discordantly; of these: 7801532 mates make up the pairs; of these: 6634581 (85.04%) aligned 0 times 535494 (6.86%) aligned exactly 1 time 631457 (8.09%) aligned >1 times 85.58% overall alignment rate Time searching: 00:27:54 Overall time: 00:27:56 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] 1275216 / 18900997 = 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 21:00:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9025734/SRX9025734.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9025734/SRX9025734.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9025734/SRX9025734.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 21:00:01: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:00:01: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:00:07: 1000000 INFO @ Wed, 08 Dec 2021 21:00:14: 2000000 INFO @ Wed, 08 Dec 2021 21:00:20: 3000000 INFO @ Wed, 08 Dec 2021 21:00:26: 4000000 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 21:00:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9025734/SRX9025734.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9025734/SRX9025734.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9025734/SRX9025734.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 21:00:32: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:00:32: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:00:32: 5000000 INFO @ Wed, 08 Dec 2021 21:00:39: 6000000 INFO @ Wed, 08 Dec 2021 21:00:40: 1000000 INFO @ Wed, 08 Dec 2021 21:00:46: 7000000 INFO @ Wed, 08 Dec 2021 21:00:47: 2000000 INFO @ Wed, 08 Dec 2021 21:00:53: 8000000 INFO @ Wed, 08 Dec 2021 21:00:54: 3000000 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 21:01:00: 9000000 INFO @ Wed, 08 Dec 2021 21:01:01: 4000000 INFO @ Wed, 08 Dec 2021 21:01:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9025734/SRX9025734.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9025734/SRX9025734.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9025734/SRX9025734.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 21:01:02: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:01:02: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:01:07: 10000000 INFO @ Wed, 08 Dec 2021 21:01:08: 5000000 INFO @ Wed, 08 Dec 2021 21:01:08: 1000000 INFO @ Wed, 08 Dec 2021 21:01:13: 11000000 INFO @ Wed, 08 Dec 2021 21:01:14: 2000000 INFO @ Wed, 08 Dec 2021 21:01:15: 6000000 INFO @ Wed, 08 Dec 2021 21:01:20: 3000000 INFO @ Wed, 08 Dec 2021 21:01:20: 12000000 INFO @ Wed, 08 Dec 2021 21:01:22: 7000000 INFO @ Wed, 08 Dec 2021 21:01:27: 4000000 INFO @ Wed, 08 Dec 2021 21:01:27: 13000000 INFO @ Wed, 08 Dec 2021 21:01:29: 8000000 INFO @ Wed, 08 Dec 2021 21:01:33: 5000000 INFO @ Wed, 08 Dec 2021 21:01:34: 14000000 INFO @ Wed, 08 Dec 2021 21:01:36: 9000000 INFO @ Wed, 08 Dec 2021 21:01:39: 6000000 INFO @ Wed, 08 Dec 2021 21:01:41: 15000000 INFO @ Wed, 08 Dec 2021 21:01:43: 10000000 INFO @ Wed, 08 Dec 2021 21:01:45: 7000000 INFO @ Wed, 08 Dec 2021 21:01:48: 16000000 INFO @ Wed, 08 Dec 2021 21:01:50: 11000000 INFO @ Wed, 08 Dec 2021 21:01:51: 8000000 INFO @ Wed, 08 Dec 2021 21:01:55: 17000000 INFO @ Wed, 08 Dec 2021 21:01:57: 12000000 INFO @ Wed, 08 Dec 2021 21:01:57: 9000000 INFO @ Wed, 08 Dec 2021 21:02:02: 18000000 INFO @ Wed, 08 Dec 2021 21:02:03: 10000000 INFO @ Wed, 08 Dec 2021 21:02:04: 13000000 INFO @ Wed, 08 Dec 2021 21:02:09: 11000000 INFO @ Wed, 08 Dec 2021 21:02:11: 14000000 INFO @ Wed, 08 Dec 2021 21:02:15: 12000000 INFO @ Wed, 08 Dec 2021 21:02:15: 19000000 INFO @ Wed, 08 Dec 2021 21:02:18: 15000000 INFO @ Wed, 08 Dec 2021 21:02:21: 13000000 INFO @ Wed, 08 Dec 2021 21:02:25: 16000000 INFO @ Wed, 08 Dec 2021 21:02:26: 20000000 INFO @ Wed, 08 Dec 2021 21:02:27: 14000000 INFO @ Wed, 08 Dec 2021 21:02:32: 17000000 INFO @ Wed, 08 Dec 2021 21:02:33: 21000000 INFO @ Wed, 08 Dec 2021 21:02:33: 15000000 INFO @ Wed, 08 Dec 2021 21:02:39: 18000000 INFO @ Wed, 08 Dec 2021 21:02:39: 16000000 INFO @ Wed, 08 Dec 2021 21:02:40: 22000000 INFO @ Wed, 08 Dec 2021 21:02:45: 17000000 INFO @ Wed, 08 Dec 2021 21:02:45: 19000000 INFO @ Wed, 08 Dec 2021 21:02:47: 23000000 INFO @ Wed, 08 Dec 2021 21:02:51: 18000000 INFO @ Wed, 08 Dec 2021 21:02:52: 20000000 INFO @ Wed, 08 Dec 2021 21:02:54: 24000000 INFO @ Wed, 08 Dec 2021 21:02:57: 19000000 INFO @ Wed, 08 Dec 2021 21:02:59: 21000000 INFO @ Wed, 08 Dec 2021 21:03:01: 25000000 INFO @ Wed, 08 Dec 2021 21:03:03: 20000000 INFO @ Wed, 08 Dec 2021 21:03:06: 22000000 INFO @ Wed, 08 Dec 2021 21:03:08: 26000000 INFO @ Wed, 08 Dec 2021 21:03:09: 21000000 INFO @ Wed, 08 Dec 2021 21:03:13: 23000000 INFO @ Wed, 08 Dec 2021 21:03:15: 27000000 INFO @ Wed, 08 Dec 2021 21:03:15: 22000000 INFO @ Wed, 08 Dec 2021 21:03:21: 24000000 INFO @ Wed, 08 Dec 2021 21:03:22: 23000000 INFO @ Wed, 08 Dec 2021 21:03:22: 28000000 INFO @ Wed, 08 Dec 2021 21:03:28: 24000000 INFO @ Wed, 08 Dec 2021 21:03:28: 29000000 INFO @ Wed, 08 Dec 2021 21:03:28: 25000000 INFO @ Wed, 08 Dec 2021 21:03:34: 25000000 INFO @ Wed, 08 Dec 2021 21:03:35: 30000000 INFO @ Wed, 08 Dec 2021 21:03:35: 26000000 INFO @ Wed, 08 Dec 2021 21:03:40: 26000000 INFO @ Wed, 08 Dec 2021 21:03:42: 31000000 INFO @ Wed, 08 Dec 2021 21:03:42: 27000000 INFO @ Wed, 08 Dec 2021 21:03:46: 27000000 INFO @ Wed, 08 Dec 2021 21:03:49: 32000000 INFO @ Wed, 08 Dec 2021 21:03:49: 28000000 INFO @ Wed, 08 Dec 2021 21:03:52: 28000000 BedGraph に変換しました。 INFO @ Wed, 08 Dec 2021 21:03:55: 29000000 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:03:56: 33000000 INFO @ Wed, 08 Dec 2021 21:03:59: 29000000 INFO @ Wed, 08 Dec 2021 21:04:01: 30000000 INFO @ Wed, 08 Dec 2021 21:04:03: 34000000 INFO @ Wed, 08 Dec 2021 21:04:05: 30000000 INFO @ Wed, 08 Dec 2021 21:04:08: 31000000 INFO @ Wed, 08 Dec 2021 21:04:10: 35000000 INFO @ Wed, 08 Dec 2021 21:04:15: 32000000 INFO @ Wed, 08 Dec 2021 21:04:16: 31000000 INFO @ Wed, 08 Dec 2021 21:04:17: 36000000 INFO @ Wed, 08 Dec 2021 21:04:22: 32000000 INFO @ Wed, 08 Dec 2021 21:04:22: 33000000 INFO @ Wed, 08 Dec 2021 21:04:23: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 21:04:23: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 21:04:23: #1 total tags in treatment: 15447012 INFO @ Wed, 08 Dec 2021 21:04:23: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:04:23: #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 21:04:23: #1 tags after filtering in treatment: 12087968 INFO @ Wed, 08 Dec 2021 21:04:23: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 08 Dec 2021 21:04:23: #1 finished! INFO @ Wed, 08 Dec 2021 21:04:23: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:04:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:04:24: #2 number of paired peaks: 117 WARNING @ Wed, 08 Dec 2021 21:04:24: 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 21:04:24: start model_add_line... INFO @ Wed, 08 Dec 2021 21:04:24: start X-correlation... INFO @ Wed, 08 Dec 2021 21:04:24: end of X-cor INFO @ Wed, 08 Dec 2021 21:04:24: #2 finished! INFO @ Wed, 08 Dec 2021 21:04:24: #2 predicted fragment length is 96 bps INFO @ Wed, 08 Dec 2021 21:04:24: #2 alternative fragment length(s) may be 12,64,70,96,182,212,231,237,265,270,323,347,498,523,558,563 bps INFO @ Wed, 08 Dec 2021 21:04:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9025734/SRX9025734.05_model.r WARNING @ Wed, 08 Dec 2021 21:04:24: #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 21:04:24: #2 You may need to consider one of the other alternative d(s): 12,64,70,96,182,212,231,237,265,270,323,347,498,523,558,563 WARNING @ Wed, 08 Dec 2021 21:04:24: #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 21:04:24: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:04:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:04:28: 33000000 INFO @ Wed, 08 Dec 2021 21:04:29: 34000000 INFO @ Wed, 08 Dec 2021 21:04:34: 34000000 INFO @ Wed, 08 Dec 2021 21:04:36: 35000000 INFO @ Wed, 08 Dec 2021 21:04:40: 35000000 INFO @ Wed, 08 Dec 2021 21:04:43: 36000000 INFO @ Wed, 08 Dec 2021 21:04:46: 36000000 INFO @ Wed, 08 Dec 2021 21:04:50: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 21:04:50: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 21:04:50: #1 total tags in treatment: 15447012 INFO @ Wed, 08 Dec 2021 21:04:50: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:04:50: #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 21:04:50: #1 tags after filtering in treatment: 12087968 INFO @ Wed, 08 Dec 2021 21:04:50: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 08 Dec 2021 21:04:50: #1 finished! INFO @ Wed, 08 Dec 2021 21:04:50: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:04:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:04:51: #2 number of paired peaks: 117 WARNING @ Wed, 08 Dec 2021 21:04:51: 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 21:04:51: start model_add_line... INFO @ Wed, 08 Dec 2021 21:04:51: start X-correlation... INFO @ Wed, 08 Dec 2021 21:04:51: end of X-cor INFO @ Wed, 08 Dec 2021 21:04:51: #2 finished! INFO @ Wed, 08 Dec 2021 21:04:51: #2 predicted fragment length is 96 bps INFO @ Wed, 08 Dec 2021 21:04:51: #2 alternative fragment length(s) may be 12,64,70,96,182,212,231,237,265,270,323,347,498,523,558,563 bps INFO @ Wed, 08 Dec 2021 21:04:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9025734/SRX9025734.10_model.r WARNING @ Wed, 08 Dec 2021 21:04:51: #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 21:04:51: #2 You may need to consider one of the other alternative d(s): 12,64,70,96,182,212,231,237,265,270,323,347,498,523,558,563 WARNING @ Wed, 08 Dec 2021 21:04:51: #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 21:04:51: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:04:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:04:51: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 21:04:51: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 21:04:51: #1 total tags in treatment: 15447012 INFO @ Wed, 08 Dec 2021 21:04:51: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:04:51: #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 21:04:52: #1 tags after filtering in treatment: 12087968 INFO @ Wed, 08 Dec 2021 21:04:52: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 08 Dec 2021 21:04:52: #1 finished! INFO @ Wed, 08 Dec 2021 21:04:52: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:04:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:04:52: #2 number of paired peaks: 117 WARNING @ Wed, 08 Dec 2021 21:04:52: 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 21:04:52: start model_add_line... INFO @ Wed, 08 Dec 2021 21:04:52: start X-correlation... INFO @ Wed, 08 Dec 2021 21:04:52: end of X-cor INFO @ Wed, 08 Dec 2021 21:04:52: #2 finished! INFO @ Wed, 08 Dec 2021 21:04:52: #2 predicted fragment length is 96 bps INFO @ Wed, 08 Dec 2021 21:04:52: #2 alternative fragment length(s) may be 12,64,70,96,182,212,231,237,265,270,323,347,498,523,558,563 bps INFO @ Wed, 08 Dec 2021 21:04:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9025734/SRX9025734.20_model.r WARNING @ Wed, 08 Dec 2021 21:04:52: #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 21:04:52: #2 You may need to consider one of the other alternative d(s): 12,64,70,96,182,212,231,237,265,270,323,347,498,523,558,563 WARNING @ Wed, 08 Dec 2021 21:04:52: #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 21:04:52: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:04:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:05:01: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:05:13: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:05:14: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:05:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9025734/SRX9025734.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:05:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9025734/SRX9025734.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:05:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9025734/SRX9025734.05_summits.bed INFO @ Wed, 08 Dec 2021 21:05:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (323 records, 4 fields): 56 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:05:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9025734/SRX9025734.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:05:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9025734/SRX9025734.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:05:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9025734/SRX9025734.20_summits.bed INFO @ Wed, 08 Dec 2021 21:05:26: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (84 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:05:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9025734/SRX9025734.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:05:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9025734/SRX9025734.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:05:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9025734/SRX9025734.10_summits.bed INFO @ Wed, 08 Dec 2021 21:05:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (187 records, 4 fields): 1 millis CompletedMACS2peakCalling