Job ID = 14160028 SRX = SRX8845644 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: 00:45:04 32516998 reads; of these: 32516998 (100.00%) were paired; of these: 19904691 (61.21%) aligned concordantly 0 times 10824983 (33.29%) aligned concordantly exactly 1 time 1787324 (5.50%) aligned concordantly >1 times ---- 19904691 pairs aligned concordantly 0 times; of these: 1806916 (9.08%) aligned discordantly 1 time ---- 18097775 pairs aligned 0 times concordantly or discordantly; of these: 36195550 mates make up the pairs; of these: 35054120 (96.85%) aligned 0 times 350113 (0.97%) aligned exactly 1 time 791317 (2.19%) aligned >1 times 46.10% overall alignment rate Time searching: 00:45:05 Overall time: 00:45:05 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] 2536376 / 14363480 = 0.1766 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 01:45:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.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 01:45:58: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:45:58: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:46:07: 1000000 INFO @ Thu, 09 Dec 2021 01:46:16: 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 @ Thu, 09 Dec 2021 01:46:26: 3000000 INFO @ Thu, 09 Dec 2021 01:46:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.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 01:46:27: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:46:27: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:46:35: 4000000 INFO @ Thu, 09 Dec 2021 01:46:40: 1000000 INFO @ Thu, 09 Dec 2021 01:46:44: 5000000 INFO @ Thu, 09 Dec 2021 01:46:53: 6000000 BedGraph に変換中... INFO @ Thu, 09 Dec 2021 01:46:54: 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 @ Thu, 09 Dec 2021 01:46:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.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 01:46:57: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:46:57: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:47:03: 7000000 INFO @ Thu, 09 Dec 2021 01:47:10: 3000000 INFO @ Thu, 09 Dec 2021 01:47:12: 1000000 INFO @ Thu, 09 Dec 2021 01:47:13: 8000000 INFO @ Thu, 09 Dec 2021 01:47:23: 9000000 INFO @ Thu, 09 Dec 2021 01:47:26: 4000000 INFO @ Thu, 09 Dec 2021 01:47:28: 2000000 INFO @ Thu, 09 Dec 2021 01:47:33: 10000000 INFO @ Thu, 09 Dec 2021 01:47:41: 5000000 INFO @ Thu, 09 Dec 2021 01:47:43: 11000000 INFO @ Thu, 09 Dec 2021 01:47:44: 3000000 INFO @ Thu, 09 Dec 2021 01:47:53: 12000000 INFO @ Thu, 09 Dec 2021 01:47:57: 6000000 INFO @ Thu, 09 Dec 2021 01:48:00: 4000000 INFO @ Thu, 09 Dec 2021 01:48:02: 13000000 INFO @ Thu, 09 Dec 2021 01:48:12: 14000000 INFO @ Thu, 09 Dec 2021 01:48:12: 7000000 INFO @ Thu, 09 Dec 2021 01:48:15: 5000000 INFO @ Thu, 09 Dec 2021 01:48:21: 15000000 INFO @ Thu, 09 Dec 2021 01:48:27: 8000000 INFO @ Thu, 09 Dec 2021 01:48:31: 6000000 INFO @ Thu, 09 Dec 2021 01:48:31: 16000000 INFO @ Thu, 09 Dec 2021 01:48:41: 17000000 INFO @ Thu, 09 Dec 2021 01:48:43: 9000000 INFO @ Thu, 09 Dec 2021 01:48:46: 7000000 INFO @ Thu, 09 Dec 2021 01:48:50: 18000000 INFO @ Thu, 09 Dec 2021 01:48:58: 10000000 INFO @ Thu, 09 Dec 2021 01:49:00: 19000000 INFO @ Thu, 09 Dec 2021 01:49:01: 8000000 INFO @ Thu, 09 Dec 2021 01:49:10: 20000000 INFO @ Thu, 09 Dec 2021 01:49:14: 11000000 INFO @ Thu, 09 Dec 2021 01:49:16: 9000000 INFO @ Thu, 09 Dec 2021 01:49:20: 21000000 INFO @ Thu, 09 Dec 2021 01:49:29: 12000000 INFO @ Thu, 09 Dec 2021 01:49:30: 22000000 INFO @ Thu, 09 Dec 2021 01:49:31: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 01:49:39: 23000000 INFO @ Thu, 09 Dec 2021 01:49:44: 13000000 INFO @ Thu, 09 Dec 2021 01:49:47: 11000000 INFO @ Thu, 09 Dec 2021 01:49:49: 24000000 INFO @ Thu, 09 Dec 2021 01:49:58: #1 tag size is determined as 125 bps INFO @ Thu, 09 Dec 2021 01:49:58: #1 tag size = 125 INFO @ Thu, 09 Dec 2021 01:49:58: #1 total tags in treatment: 10389406 INFO @ Thu, 09 Dec 2021 01:49:58: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:49:58: #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 01:49:58: #1 tags after filtering in treatment: 7311468 INFO @ Thu, 09 Dec 2021 01:49:58: #1 Redundant rate of treatment: 0.30 INFO @ Thu, 09 Dec 2021 01:49:58: #1 finished! INFO @ Thu, 09 Dec 2021 01:49:58: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:49:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:49:59: #2 number of paired peaks: 1169 INFO @ Thu, 09 Dec 2021 01:49:59: start model_add_line... INFO @ Thu, 09 Dec 2021 01:49:59: start X-correlation... INFO @ Thu, 09 Dec 2021 01:49:59: end of X-cor INFO @ Thu, 09 Dec 2021 01:49:59: #2 finished! INFO @ Thu, 09 Dec 2021 01:49:59: #2 predicted fragment length is 241 bps INFO @ Thu, 09 Dec 2021 01:49:59: #2 alternative fragment length(s) may be 241 bps INFO @ Thu, 09 Dec 2021 01:49:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.05_model.r WARNING @ Thu, 09 Dec 2021 01:49:59: #2 Since the d (241) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:49:59: #2 You may need to consider one of the other alternative d(s): 241 WARNING @ Thu, 09 Dec 2021 01:49:59: #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 01:49:59: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:49:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:50:00: 14000000 INFO @ Thu, 09 Dec 2021 01:50:02: 12000000 INFO @ Thu, 09 Dec 2021 01:50:15: 15000000 INFO @ Thu, 09 Dec 2021 01:50:17: 13000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 01:50:24: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:50:30: 16000000 INFO @ Thu, 09 Dec 2021 01:50:32: 14000000 INFO @ Thu, 09 Dec 2021 01:50:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.05_peaks.xls INFO @ Thu, 09 Dec 2021 01:50:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:50:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.05_summits.bed INFO @ Thu, 09 Dec 2021 01:50:36: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (6746 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:50:45: 17000000 INFO @ Thu, 09 Dec 2021 01:50:47: 15000000 INFO @ Thu, 09 Dec 2021 01:51:00: 18000000 INFO @ Thu, 09 Dec 2021 01:51:02: 16000000 INFO @ Thu, 09 Dec 2021 01:51:14: 19000000 INFO @ Thu, 09 Dec 2021 01:51:17: 17000000 INFO @ Thu, 09 Dec 2021 01:51:29: 20000000 INFO @ Thu, 09 Dec 2021 01:51:31: 18000000 INFO @ Thu, 09 Dec 2021 01:51:44: 21000000 INFO @ Thu, 09 Dec 2021 01:51:46: 19000000 INFO @ Thu, 09 Dec 2021 01:51:59: 22000000 INFO @ Thu, 09 Dec 2021 01:52:01: 20000000 INFO @ Thu, 09 Dec 2021 01:52:13: 23000000 INFO @ Thu, 09 Dec 2021 01:52:16: 21000000 INFO @ Thu, 09 Dec 2021 01:52:28: 24000000 INFO @ Thu, 09 Dec 2021 01:52:31: 22000000 INFO @ Thu, 09 Dec 2021 01:52:41: #1 tag size is determined as 125 bps INFO @ Thu, 09 Dec 2021 01:52:41: #1 tag size = 125 INFO @ Thu, 09 Dec 2021 01:52:41: #1 total tags in treatment: 10389406 INFO @ Thu, 09 Dec 2021 01:52:41: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:52:41: #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 01:52:41: #1 tags after filtering in treatment: 7311468 INFO @ Thu, 09 Dec 2021 01:52:41: #1 Redundant rate of treatment: 0.30 INFO @ Thu, 09 Dec 2021 01:52:41: #1 finished! INFO @ Thu, 09 Dec 2021 01:52:41: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:52:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:52:42: #2 number of paired peaks: 1169 INFO @ Thu, 09 Dec 2021 01:52:42: start model_add_line... INFO @ Thu, 09 Dec 2021 01:52:42: start X-correlation... INFO @ Thu, 09 Dec 2021 01:52:42: end of X-cor INFO @ Thu, 09 Dec 2021 01:52:42: #2 finished! INFO @ Thu, 09 Dec 2021 01:52:42: #2 predicted fragment length is 241 bps INFO @ Thu, 09 Dec 2021 01:52:42: #2 alternative fragment length(s) may be 241 bps INFO @ Thu, 09 Dec 2021 01:52:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.10_model.r WARNING @ Thu, 09 Dec 2021 01:52:42: #2 Since the d (241) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:52:42: #2 You may need to consider one of the other alternative d(s): 241 WARNING @ Thu, 09 Dec 2021 01:52:42: #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 01:52:42: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:52:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:52:45: 23000000 INFO @ Thu, 09 Dec 2021 01:52:57: 24000000 INFO @ Thu, 09 Dec 2021 01:53:07: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:53:09: #1 tag size is determined as 125 bps INFO @ Thu, 09 Dec 2021 01:53:09: #1 tag size = 125 INFO @ Thu, 09 Dec 2021 01:53:09: #1 total tags in treatment: 10389406 INFO @ Thu, 09 Dec 2021 01:53:09: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:53:09: #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 01:53:09: #1 tags after filtering in treatment: 7311468 INFO @ Thu, 09 Dec 2021 01:53:09: #1 Redundant rate of treatment: 0.30 INFO @ Thu, 09 Dec 2021 01:53:09: #1 finished! INFO @ Thu, 09 Dec 2021 01:53:09: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:53:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:53:10: #2 number of paired peaks: 1169 INFO @ Thu, 09 Dec 2021 01:53:10: start model_add_line... INFO @ Thu, 09 Dec 2021 01:53:10: start X-correlation... INFO @ Thu, 09 Dec 2021 01:53:10: end of X-cor INFO @ Thu, 09 Dec 2021 01:53:10: #2 finished! INFO @ Thu, 09 Dec 2021 01:53:10: #2 predicted fragment length is 241 bps INFO @ Thu, 09 Dec 2021 01:53:10: #2 alternative fragment length(s) may be 241 bps INFO @ Thu, 09 Dec 2021 01:53:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.20_model.r WARNING @ Thu, 09 Dec 2021 01:53:10: #2 Since the d (241) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:53:10: #2 You may need to consider one of the other alternative d(s): 241 WARNING @ Thu, 09 Dec 2021 01:53:10: #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 01:53:10: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:53:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:53:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.10_peaks.xls INFO @ Thu, 09 Dec 2021 01:53:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:53:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.10_summits.bed INFO @ Thu, 09 Dec 2021 01:53:20: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4182 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:53:35: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:53:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.20_peaks.xls INFO @ Thu, 09 Dec 2021 01:53:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:53:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845644/SRX8845644.20_summits.bed INFO @ Thu, 09 Dec 2021 01:53:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1892 records, 4 fields): 7 millis CompletedMACS2peakCalling