Job ID = 14159933 SRX = SRX8845637 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:32:12 46179915 reads; of these: 46179915 (100.00%) were paired; of these: 9412481 (20.38%) aligned concordantly 0 times 29786329 (64.50%) aligned concordantly exactly 1 time 6981105 (15.12%) aligned concordantly >1 times ---- 9412481 pairs aligned concordantly 0 times; of these: 872617 (9.27%) aligned discordantly 1 time ---- 8539864 pairs aligned 0 times concordantly or discordantly; of these: 17079728 mates make up the pairs; of these: 16207320 (94.89%) aligned 0 times 361375 (2.12%) aligned exactly 1 time 511033 (2.99%) aligned >1 times 82.45% overall alignment rate Time searching: 00:32:13 Overall time: 00:32:13 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 32 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] 18216223 / 37477460 = 0.4861 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 01:22:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.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 01:22:23: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:22:23: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:22:28: 1000000 INFO @ Thu, 09 Dec 2021 01:22:33: 2000000 INFO @ Thu, 09 Dec 2021 01:22:38: 3000000 INFO @ Thu, 09 Dec 2021 01:22:43: 4000000 INFO @ Thu, 09 Dec 2021 01:22:47: 5000000 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 01:22:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.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 01:22:51: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:22:51: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:22:52: 6000000 INFO @ Thu, 09 Dec 2021 01:22:56: 1000000 INFO @ Thu, 09 Dec 2021 01:22:57: 7000000 INFO @ Thu, 09 Dec 2021 01:23:01: 2000000 INFO @ Thu, 09 Dec 2021 01:23:02: 8000000 INFO @ Thu, 09 Dec 2021 01:23:06: 3000000 INFO @ Thu, 09 Dec 2021 01:23:07: 9000000 INFO @ Thu, 09 Dec 2021 01:23:11: 4000000 INFO @ Thu, 09 Dec 2021 01:23:11: 10000000 INFO @ Thu, 09 Dec 2021 01:23:16: 5000000 INFO @ Thu, 09 Dec 2021 01:23:16: 11000000 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 01:23:21: 6000000 INFO @ Thu, 09 Dec 2021 01:23:21: 12000000 INFO @ Thu, 09 Dec 2021 01:23:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.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 01:23:21: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:23:21: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:23:25: 7000000 INFO @ Thu, 09 Dec 2021 01:23:26: 13000000 INFO @ Thu, 09 Dec 2021 01:23:26: 1000000 INFO @ Thu, 09 Dec 2021 01:23:30: 8000000 INFO @ Thu, 09 Dec 2021 01:23:31: 14000000 INFO @ Thu, 09 Dec 2021 01:23:31: 2000000 INFO @ Thu, 09 Dec 2021 01:23:35: 9000000 INFO @ Thu, 09 Dec 2021 01:23:36: 15000000 INFO @ Thu, 09 Dec 2021 01:23:36: 3000000 INFO @ Thu, 09 Dec 2021 01:23:40: 10000000 INFO @ Thu, 09 Dec 2021 01:23:40: 16000000 INFO @ Thu, 09 Dec 2021 01:23:41: 4000000 INFO @ Thu, 09 Dec 2021 01:23:45: 11000000 INFO @ Thu, 09 Dec 2021 01:23:45: 17000000 INFO @ Thu, 09 Dec 2021 01:23:46: 5000000 INFO @ Thu, 09 Dec 2021 01:23:50: 12000000 INFO @ Thu, 09 Dec 2021 01:23:50: 18000000 INFO @ Thu, 09 Dec 2021 01:23:50: 6000000 INFO @ Thu, 09 Dec 2021 01:23:55: 13000000 INFO @ Thu, 09 Dec 2021 01:23:55: 19000000 INFO @ Thu, 09 Dec 2021 01:23:55: 7000000 INFO @ Thu, 09 Dec 2021 01:24:00: 14000000 INFO @ Thu, 09 Dec 2021 01:24:00: 20000000 INFO @ Thu, 09 Dec 2021 01:24:00: 8000000 INFO @ Thu, 09 Dec 2021 01:24:05: 15000000 INFO @ Thu, 09 Dec 2021 01:24:05: 21000000 INFO @ Thu, 09 Dec 2021 01:24:05: 9000000 INFO @ Thu, 09 Dec 2021 01:24:10: 22000000 INFO @ Thu, 09 Dec 2021 01:24:10: 10000000 INFO @ Thu, 09 Dec 2021 01:24:10: 16000000 INFO @ Thu, 09 Dec 2021 01:24:14: 23000000 INFO @ Thu, 09 Dec 2021 01:24:15: 11000000 INFO @ Thu, 09 Dec 2021 01:24:15: 17000000 INFO @ Thu, 09 Dec 2021 01:24:19: 24000000 INFO @ Thu, 09 Dec 2021 01:24:19: 12000000 INFO @ Thu, 09 Dec 2021 01:24:20: 18000000 INFO @ Thu, 09 Dec 2021 01:24:24: 13000000 INFO @ Thu, 09 Dec 2021 01:24:24: 25000000 INFO @ Thu, 09 Dec 2021 01:24:25: 19000000 INFO @ Thu, 09 Dec 2021 01:24:29: 14000000 INFO @ Thu, 09 Dec 2021 01:24:29: 26000000 INFO @ Thu, 09 Dec 2021 01:24:29: 20000000 INFO @ Thu, 09 Dec 2021 01:24:34: 15000000 INFO @ Thu, 09 Dec 2021 01:24:34: 27000000 INFO @ Thu, 09 Dec 2021 01:24:34: 21000000 INFO @ Thu, 09 Dec 2021 01:24:38: 16000000 INFO @ Thu, 09 Dec 2021 01:24:39: 28000000 INFO @ Thu, 09 Dec 2021 01:24:39: 22000000 INFO @ Thu, 09 Dec 2021 01:24:43: 17000000 INFO @ Thu, 09 Dec 2021 01:24:43: 29000000 INFO @ Thu, 09 Dec 2021 01:24:44: 23000000 INFO @ Thu, 09 Dec 2021 01:24:48: 18000000 INFO @ Thu, 09 Dec 2021 01:24:48: 30000000 INFO @ Thu, 09 Dec 2021 01:24:49: 24000000 INFO @ Thu, 09 Dec 2021 01:24:53: 19000000 INFO @ Thu, 09 Dec 2021 01:24:53: 31000000 INFO @ Thu, 09 Dec 2021 01:24:53: 25000000 INFO @ Thu, 09 Dec 2021 01:24:58: 20000000 INFO @ Thu, 09 Dec 2021 01:24:58: 32000000 INFO @ Thu, 09 Dec 2021 01:24:58: 26000000 INFO @ Thu, 09 Dec 2021 01:25:02: 21000000 INFO @ Thu, 09 Dec 2021 01:25:03: 33000000 INFO @ Thu, 09 Dec 2021 01:25:03: 27000000 INFO @ Thu, 09 Dec 2021 01:25:07: 22000000 INFO @ Thu, 09 Dec 2021 01:25:08: 34000000 INFO @ Thu, 09 Dec 2021 01:25:08: 28000000 INFO @ Thu, 09 Dec 2021 01:25:12: 23000000 INFO @ Thu, 09 Dec 2021 01:25:13: 29000000 INFO @ Thu, 09 Dec 2021 01:25:13: 35000000 INFO @ Thu, 09 Dec 2021 01:25:17: 24000000 INFO @ Thu, 09 Dec 2021 01:25:18: 30000000 INFO @ Thu, 09 Dec 2021 01:25:18: 36000000 INFO @ Thu, 09 Dec 2021 01:25:22: 25000000 INFO @ Thu, 09 Dec 2021 01:25:22: 31000000 INFO @ Thu, 09 Dec 2021 01:25:23: 37000000 INFO @ Thu, 09 Dec 2021 01:25:26: 26000000 INFO @ Thu, 09 Dec 2021 01:25:27: 32000000 INFO @ Thu, 09 Dec 2021 01:25:28: 38000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 01:25:31: 27000000 INFO @ Thu, 09 Dec 2021 01:25:32: 33000000 INFO @ Thu, 09 Dec 2021 01:25:33: 39000000 INFO @ Thu, 09 Dec 2021 01:25:36: 28000000 INFO @ Thu, 09 Dec 2021 01:25:36: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 01:25:36: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 01:25:36: #1 total tags in treatment: 18825305 INFO @ Thu, 09 Dec 2021 01:25:36: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:25:36: #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 01:25:37: #1 tags after filtering in treatment: 10853222 INFO @ Thu, 09 Dec 2021 01:25:37: #1 Redundant rate of treatment: 0.42 INFO @ Thu, 09 Dec 2021 01:25:37: #1 finished! INFO @ Thu, 09 Dec 2021 01:25:37: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:25:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:25:37: 34000000 INFO @ Thu, 09 Dec 2021 01:25:37: #2 number of paired peaks: 1162 INFO @ Thu, 09 Dec 2021 01:25:37: start model_add_line... INFO @ Thu, 09 Dec 2021 01:25:38: start X-correlation... INFO @ Thu, 09 Dec 2021 01:25:38: end of X-cor INFO @ Thu, 09 Dec 2021 01:25:38: #2 finished! INFO @ Thu, 09 Dec 2021 01:25:38: #2 predicted fragment length is 79 bps INFO @ Thu, 09 Dec 2021 01:25:38: #2 alternative fragment length(s) may be 79 bps INFO @ Thu, 09 Dec 2021 01:25:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.05_model.r WARNING @ Thu, 09 Dec 2021 01:25:38: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:25:38: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Thu, 09 Dec 2021 01:25:38: #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 01:25:38: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:25:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:25:41: 29000000 INFO @ Thu, 09 Dec 2021 01:25:42: 35000000 INFO @ Thu, 09 Dec 2021 01:25:46: 30000000 INFO @ Thu, 09 Dec 2021 01:25:47: 36000000 INFO @ Thu, 09 Dec 2021 01:25:51: 31000000 INFO @ Thu, 09 Dec 2021 01:25:52: 37000000 INFO @ Thu, 09 Dec 2021 01:25:55: 32000000 INFO @ Thu, 09 Dec 2021 01:25:57: 38000000 INFO @ Thu, 09 Dec 2021 01:25:58: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:26:00: 33000000 INFO @ Thu, 09 Dec 2021 01:26:01: 39000000 INFO @ Thu, 09 Dec 2021 01:26:05: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 01:26:05: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 01:26:05: #1 total tags in treatment: 18825305 INFO @ Thu, 09 Dec 2021 01:26:05: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:26:05: #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 01:26:05: 34000000 INFO @ Thu, 09 Dec 2021 01:26:05: #1 tags after filtering in treatment: 10853222 INFO @ Thu, 09 Dec 2021 01:26:05: #1 Redundant rate of treatment: 0.42 INFO @ Thu, 09 Dec 2021 01:26:05: #1 finished! INFO @ Thu, 09 Dec 2021 01:26:05: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:26:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:26:06: #2 number of paired peaks: 1162 INFO @ Thu, 09 Dec 2021 01:26:06: start model_add_line... INFO @ Thu, 09 Dec 2021 01:26:06: start X-correlation... INFO @ Thu, 09 Dec 2021 01:26:06: end of X-cor INFO @ Thu, 09 Dec 2021 01:26:06: #2 finished! INFO @ Thu, 09 Dec 2021 01:26:06: #2 predicted fragment length is 79 bps INFO @ Thu, 09 Dec 2021 01:26:06: #2 alternative fragment length(s) may be 79 bps INFO @ Thu, 09 Dec 2021 01:26:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.10_model.r WARNING @ Thu, 09 Dec 2021 01:26:06: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:26:06: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Thu, 09 Dec 2021 01:26:06: #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 01:26:06: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:26:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:26:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.05_peaks.xls INFO @ Thu, 09 Dec 2021 01:26:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:26:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.05_summits.bed INFO @ Thu, 09 Dec 2021 01:26:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (11586 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:26:10: 35000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 01:26:14: 36000000 INFO @ Thu, 09 Dec 2021 01:26:19: 37000000 INFO @ Thu, 09 Dec 2021 01:26:24: 38000000 INFO @ Thu, 09 Dec 2021 01:26:28: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:26:28: 39000000 INFO @ Thu, 09 Dec 2021 01:26:32: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 01:26:32: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 01:26:32: #1 total tags in treatment: 18825305 INFO @ Thu, 09 Dec 2021 01:26:32: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:26:32: #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 01:26:32: #1 tags after filtering in treatment: 10853222 INFO @ Thu, 09 Dec 2021 01:26:32: #1 Redundant rate of treatment: 0.42 INFO @ Thu, 09 Dec 2021 01:26:32: #1 finished! INFO @ Thu, 09 Dec 2021 01:26:32: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:26:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:26:33: #2 number of paired peaks: 1162 INFO @ Thu, 09 Dec 2021 01:26:33: start model_add_line... INFO @ Thu, 09 Dec 2021 01:26:33: start X-correlation... INFO @ Thu, 09 Dec 2021 01:26:33: end of X-cor INFO @ Thu, 09 Dec 2021 01:26:33: #2 finished! INFO @ Thu, 09 Dec 2021 01:26:33: #2 predicted fragment length is 79 bps INFO @ Thu, 09 Dec 2021 01:26:33: #2 alternative fragment length(s) may be 79 bps INFO @ Thu, 09 Dec 2021 01:26:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.20_model.r WARNING @ Thu, 09 Dec 2021 01:26:33: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:26:33: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Thu, 09 Dec 2021 01:26:33: #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 01:26:33: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:26:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:26:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.10_peaks.xls INFO @ Thu, 09 Dec 2021 01:26:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:26:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.10_summits.bed INFO @ Thu, 09 Dec 2021 01:26:39: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (8046 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:26:54: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:27:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.20_peaks.xls INFO @ Thu, 09 Dec 2021 01:27:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:27:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845637/SRX8845637.20_summits.bed INFO @ Thu, 09 Dec 2021 01:27:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4343 records, 4 fields): 5 millis CompletedMACS2peakCalling