Job ID = 14160648 SRX = SRX7756572 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: 00:27:56 20228470 reads; of these: 20228470 (100.00%) were paired; of these: 3822912 (18.90%) aligned concordantly 0 times 14074814 (69.58%) aligned concordantly exactly 1 time 2330744 (11.52%) aligned concordantly >1 times ---- 3822912 pairs aligned concordantly 0 times; of these: 1598896 (41.82%) aligned discordantly 1 time ---- 2224016 pairs aligned 0 times concordantly or discordantly; of these: 4448032 mates make up the pairs; of these: 3571248 (80.29%) aligned 0 times 445259 (10.01%) aligned exactly 1 time 431525 (9.70%) aligned >1 times 91.17% overall alignment rate Time searching: 00:27:56 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 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] 361048 / 17945599 = 0.0201 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 @ Thu, 09 Dec 2021 04:09:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.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 @ Thu, 09 Dec 2021 04:09:51: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:09:51: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:09:57: 1000000 INFO @ Thu, 09 Dec 2021 04:10:03: 2000000 INFO @ Thu, 09 Dec 2021 04:10:09: 3000000 INFO @ Thu, 09 Dec 2021 04:10:15: 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 @ Thu, 09 Dec 2021 04:10:21: 5000000 INFO @ Thu, 09 Dec 2021 04:10:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.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 @ Thu, 09 Dec 2021 04:10:22: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:10:22: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:10:29: 6000000 INFO @ Thu, 09 Dec 2021 04:10:30: 1000000 INFO @ Thu, 09 Dec 2021 04:10:37: 7000000 INFO @ Thu, 09 Dec 2021 04:10:39: 2000000 INFO @ Thu, 09 Dec 2021 04:10:45: 8000000 INFO @ Thu, 09 Dec 2021 04:10:47: 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 @ Thu, 09 Dec 2021 04:10:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.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 @ Thu, 09 Dec 2021 04:10:51: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:10:51: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:10:53: 9000000 INFO @ Thu, 09 Dec 2021 04:10:55: 4000000 INFO @ Thu, 09 Dec 2021 04:10:59: 1000000 INFO @ Thu, 09 Dec 2021 04:11:01: 10000000 INFO @ Thu, 09 Dec 2021 04:11:04: 5000000 INFO @ Thu, 09 Dec 2021 04:11:07: 2000000 INFO @ Thu, 09 Dec 2021 04:11:09: 11000000 INFO @ Thu, 09 Dec 2021 04:11:12: 6000000 INFO @ Thu, 09 Dec 2021 04:11:15: 3000000 INFO @ Thu, 09 Dec 2021 04:11:17: 12000000 INFO @ Thu, 09 Dec 2021 04:11:21: 7000000 INFO @ Thu, 09 Dec 2021 04:11:23: 4000000 INFO @ Thu, 09 Dec 2021 04:11:25: 13000000 INFO @ Thu, 09 Dec 2021 04:11:29: 8000000 INFO @ Thu, 09 Dec 2021 04:11:31: 5000000 INFO @ Thu, 09 Dec 2021 04:11:33: 14000000 INFO @ Thu, 09 Dec 2021 04:11:37: 9000000 INFO @ Thu, 09 Dec 2021 04:11:39: 6000000 INFO @ Thu, 09 Dec 2021 04:11:41: 15000000 INFO @ Thu, 09 Dec 2021 04:11:46: 10000000 INFO @ Thu, 09 Dec 2021 04:11:47: 7000000 INFO @ Thu, 09 Dec 2021 04:11:49: 16000000 INFO @ Thu, 09 Dec 2021 04:11:54: 11000000 INFO @ Thu, 09 Dec 2021 04:11:55: 8000000 INFO @ Thu, 09 Dec 2021 04:11:57: 17000000 INFO @ Thu, 09 Dec 2021 04:12:03: 9000000 INFO @ Thu, 09 Dec 2021 04:12:03: 12000000 INFO @ Thu, 09 Dec 2021 04:12:05: 18000000 INFO @ Thu, 09 Dec 2021 04:12:11: 10000000 INFO @ Thu, 09 Dec 2021 04:12:11: 13000000 INFO @ Thu, 09 Dec 2021 04:12:13: 19000000 INFO @ Thu, 09 Dec 2021 04:12:18: 11000000 INFO @ Thu, 09 Dec 2021 04:12:20: 14000000 INFO @ Thu, 09 Dec 2021 04:12:21: 20000000 INFO @ Thu, 09 Dec 2021 04:12:26: 12000000 INFO @ Thu, 09 Dec 2021 04:12:28: 15000000 INFO @ Thu, 09 Dec 2021 04:12:29: 21000000 INFO @ Thu, 09 Dec 2021 04:12:34: 13000000 INFO @ Thu, 09 Dec 2021 04:12:36: 16000000 INFO @ Thu, 09 Dec 2021 04:12:37: 22000000 INFO @ Thu, 09 Dec 2021 04:12:42: 14000000 INFO @ Thu, 09 Dec 2021 04:12:45: 17000000 INFO @ Thu, 09 Dec 2021 04:12:45: 23000000 INFO @ Thu, 09 Dec 2021 04:12:50: 15000000 INFO @ Thu, 09 Dec 2021 04:12:53: 24000000 INFO @ Thu, 09 Dec 2021 04:12:53: 18000000 INFO @ Thu, 09 Dec 2021 04:12:58: 16000000 INFO @ Thu, 09 Dec 2021 04:13:01: 25000000 INFO @ Thu, 09 Dec 2021 04:13:02: 19000000 INFO @ Thu, 09 Dec 2021 04:13:06: 17000000 INFO @ Thu, 09 Dec 2021 04:13:09: 26000000 INFO @ Thu, 09 Dec 2021 04:13:10: 20000000 INFO @ Thu, 09 Dec 2021 04:13:14: 18000000 INFO @ Thu, 09 Dec 2021 04:13:17: 27000000 INFO @ Thu, 09 Dec 2021 04:13:18: 21000000 INFO @ Thu, 09 Dec 2021 04:13:22: 19000000 INFO @ Thu, 09 Dec 2021 04:13:25: 28000000 INFO @ Thu, 09 Dec 2021 04:13:27: 22000000 INFO @ Thu, 09 Dec 2021 04:13:30: 20000000 INFO @ Thu, 09 Dec 2021 04:13:33: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:13:35: 23000000 INFO @ Thu, 09 Dec 2021 04:13:38: 21000000 INFO @ Thu, 09 Dec 2021 04:13:41: 30000000 INFO @ Thu, 09 Dec 2021 04:13:43: 24000000 INFO @ Thu, 09 Dec 2021 04:13:46: 22000000 INFO @ Thu, 09 Dec 2021 04:13:49: 31000000 INFO @ Thu, 09 Dec 2021 04:13:52: 25000000 INFO @ Thu, 09 Dec 2021 04:13:54: 23000000 INFO @ Thu, 09 Dec 2021 04:13:57: 32000000 INFO @ Thu, 09 Dec 2021 04:14:00: 26000000 INFO @ Thu, 09 Dec 2021 04:14:02: 24000000 INFO @ Thu, 09 Dec 2021 04:14:05: 33000000 INFO @ Thu, 09 Dec 2021 04:14:09: 27000000 INFO @ Thu, 09 Dec 2021 04:14:10: 25000000 INFO @ Thu, 09 Dec 2021 04:14:13: 34000000 INFO @ Thu, 09 Dec 2021 04:14:17: 28000000 INFO @ Thu, 09 Dec 2021 04:14:18: 26000000 INFO @ Thu, 09 Dec 2021 04:14:21: 35000000 INFO @ Thu, 09 Dec 2021 04:14:25: 29000000 INFO @ Thu, 09 Dec 2021 04:14:26: 27000000 INFO @ Thu, 09 Dec 2021 04:14:29: 36000000 INFO @ Thu, 09 Dec 2021 04:14:31: #1 tag size is determined as 101 bps INFO @ Thu, 09 Dec 2021 04:14:31: #1 tag size = 101 INFO @ Thu, 09 Dec 2021 04:14:31: #1 total tags in treatment: 16063416 INFO @ Thu, 09 Dec 2021 04:14:31: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:14:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:14:31: #1 tags after filtering in treatment: 14412245 INFO @ Thu, 09 Dec 2021 04:14:31: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 04:14:31: #1 finished! INFO @ Thu, 09 Dec 2021 04:14:31: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:14:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:14:32: #2 number of paired peaks: 278 WARNING @ Thu, 09 Dec 2021 04:14:32: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Thu, 09 Dec 2021 04:14:32: start model_add_line... INFO @ Thu, 09 Dec 2021 04:14:32: start X-correlation... INFO @ Thu, 09 Dec 2021 04:14:32: end of X-cor INFO @ Thu, 09 Dec 2021 04:14:32: #2 finished! INFO @ Thu, 09 Dec 2021 04:14:32: #2 predicted fragment length is 176 bps INFO @ Thu, 09 Dec 2021 04:14:32: #2 alternative fragment length(s) may be 176 bps INFO @ Thu, 09 Dec 2021 04:14:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.05_model.r WARNING @ Thu, 09 Dec 2021 04:14:32: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:14:32: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Thu, 09 Dec 2021 04:14:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:14:32: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:14:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:14:34: 30000000 INFO @ Thu, 09 Dec 2021 04:14:34: 28000000 INFO @ Thu, 09 Dec 2021 04:14:42: 29000000 INFO @ Thu, 09 Dec 2021 04:14:42: 31000000 INFO @ Thu, 09 Dec 2021 04:14:50: 30000000 INFO @ Thu, 09 Dec 2021 04:14:50: 32000000 INFO @ Thu, 09 Dec 2021 04:14:57: 31000000 INFO @ Thu, 09 Dec 2021 04:14:59: 33000000 INFO @ Thu, 09 Dec 2021 04:15:01: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:15:05: 32000000 INFO @ Thu, 09 Dec 2021 04:15:07: 34000000 INFO @ Thu, 09 Dec 2021 04:15:12: 33000000 INFO @ Thu, 09 Dec 2021 04:15:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:15:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:15:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.05_summits.bed INFO @ Thu, 09 Dec 2021 04:15:15: Done! INFO @ Thu, 09 Dec 2021 04:15:15: 35000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (423 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:15:20: 34000000 INFO @ Thu, 09 Dec 2021 04:15:24: 36000000 INFO @ Thu, 09 Dec 2021 04:15:25: #1 tag size is determined as 101 bps INFO @ Thu, 09 Dec 2021 04:15:25: #1 tag size = 101 INFO @ Thu, 09 Dec 2021 04:15:25: #1 total tags in treatment: 16063416 INFO @ Thu, 09 Dec 2021 04:15:25: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:15:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:15:25: #1 tags after filtering in treatment: 14412245 INFO @ Thu, 09 Dec 2021 04:15:25: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 04:15:25: #1 finished! INFO @ Thu, 09 Dec 2021 04:15:25: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:15:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:15:26: #2 number of paired peaks: 278 WARNING @ Thu, 09 Dec 2021 04:15:26: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Thu, 09 Dec 2021 04:15:26: start model_add_line... INFO @ Thu, 09 Dec 2021 04:15:27: start X-correlation... INFO @ Thu, 09 Dec 2021 04:15:27: end of X-cor INFO @ Thu, 09 Dec 2021 04:15:27: #2 finished! INFO @ Thu, 09 Dec 2021 04:15:27: #2 predicted fragment length is 176 bps INFO @ Thu, 09 Dec 2021 04:15:27: #2 alternative fragment length(s) may be 176 bps INFO @ Thu, 09 Dec 2021 04:15:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.10_model.r WARNING @ Thu, 09 Dec 2021 04:15:27: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:15:27: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Thu, 09 Dec 2021 04:15:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:15:27: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:15:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:15:28: 35000000 INFO @ Thu, 09 Dec 2021 04:15:36: 36000000 INFO @ Thu, 09 Dec 2021 04:15:38: #1 tag size is determined as 101 bps INFO @ Thu, 09 Dec 2021 04:15:38: #1 tag size = 101 INFO @ Thu, 09 Dec 2021 04:15:38: #1 total tags in treatment: 16063416 INFO @ Thu, 09 Dec 2021 04:15:38: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:15:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:15:38: #1 tags after filtering in treatment: 14412245 INFO @ Thu, 09 Dec 2021 04:15:38: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 04:15:38: #1 finished! INFO @ Thu, 09 Dec 2021 04:15:38: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:15:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:15:39: #2 number of paired peaks: 278 WARNING @ Thu, 09 Dec 2021 04:15:39: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Thu, 09 Dec 2021 04:15:39: start model_add_line... INFO @ Thu, 09 Dec 2021 04:15:39: start X-correlation... INFO @ Thu, 09 Dec 2021 04:15:39: end of X-cor INFO @ Thu, 09 Dec 2021 04:15:39: #2 finished! INFO @ Thu, 09 Dec 2021 04:15:39: #2 predicted fragment length is 176 bps INFO @ Thu, 09 Dec 2021 04:15:39: #2 alternative fragment length(s) may be 176 bps INFO @ Thu, 09 Dec 2021 04:15:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.20_model.r WARNING @ Thu, 09 Dec 2021 04:15:40: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:15:40: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Thu, 09 Dec 2021 04:15:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:15:40: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:15:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:15:54: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:16:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:16:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:16:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.10_summits.bed INFO @ Thu, 09 Dec 2021 04:16:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (320 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:16:12: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:16:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:16:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:16:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7756572/SRX7756572.20_summits.bed INFO @ Thu, 09 Dec 2021 04:16:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (217 records, 4 fields): 1 millis CompletedMACS2peakCalling