Job ID = 12265438 SRX = SRX2333001 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:31:45 21992224 reads; of these: 21992224 (100.00%) were paired; of these: 7535562 (34.26%) aligned concordantly 0 times 11863698 (53.94%) aligned concordantly exactly 1 time 2592964 (11.79%) aligned concordantly >1 times ---- 7535562 pairs aligned concordantly 0 times; of these: 3510861 (46.59%) aligned discordantly 1 time ---- 4024701 pairs aligned 0 times concordantly or discordantly; of these: 8049402 mates make up the pairs; of these: 6490130 (80.63%) aligned 0 times 636438 (7.91%) aligned exactly 1 time 922834 (11.46%) aligned >1 times 85.24% overall alignment rate Time searching: 00:31:46 Overall time: 00:31:46 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] 1778311 / 17867022 = 0.0995 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:50:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.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 @ Sat, 03 Apr 2021 07:50:52: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:50:52: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:50:59: 1000000 INFO @ Sat, 03 Apr 2021 07:51:06: 2000000 INFO @ Sat, 03 Apr 2021 07:51:14: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:51:21: 4000000 INFO @ Sat, 03 Apr 2021 07:51:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.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 @ Sat, 03 Apr 2021 07:51:22: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:51:22: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:51:29: 5000000 INFO @ Sat, 03 Apr 2021 07:51:30: 1000000 INFO @ Sat, 03 Apr 2021 07:51:37: 6000000 INFO @ Sat, 03 Apr 2021 07:51:38: 2000000 INFO @ Sat, 03 Apr 2021 07:51:46: 7000000 INFO @ Sat, 03 Apr 2021 07:51:46: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:51:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.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 @ Sat, 03 Apr 2021 07:51:52: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:51:52: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:51:54: 8000000 INFO @ Sat, 03 Apr 2021 07:51:54: 4000000 INFO @ Sat, 03 Apr 2021 07:52:00: 1000000 INFO @ Sat, 03 Apr 2021 07:52:02: 9000000 INFO @ Sat, 03 Apr 2021 07:52:02: 5000000 INFO @ Sat, 03 Apr 2021 07:52:08: 2000000 INFO @ Sat, 03 Apr 2021 07:52:11: 10000000 INFO @ Sat, 03 Apr 2021 07:52:11: 6000000 INFO @ Sat, 03 Apr 2021 07:52:17: 3000000 INFO @ Sat, 03 Apr 2021 07:52:19: 11000000 INFO @ Sat, 03 Apr 2021 07:52:19: 7000000 INFO @ Sat, 03 Apr 2021 07:52:25: 4000000 INFO @ Sat, 03 Apr 2021 07:52:28: 12000000 INFO @ Sat, 03 Apr 2021 07:52:28: 8000000 INFO @ Sat, 03 Apr 2021 07:52:33: 5000000 INFO @ Sat, 03 Apr 2021 07:52:36: 9000000 INFO @ Sat, 03 Apr 2021 07:52:36: 13000000 INFO @ Sat, 03 Apr 2021 07:52:42: 6000000 INFO @ Sat, 03 Apr 2021 07:52:45: 14000000 INFO @ Sat, 03 Apr 2021 07:52:45: 10000000 INFO @ Sat, 03 Apr 2021 07:52:50: 7000000 INFO @ Sat, 03 Apr 2021 07:52:53: 15000000 INFO @ Sat, 03 Apr 2021 07:52:53: 11000000 INFO @ Sat, 03 Apr 2021 07:52:58: 8000000 INFO @ Sat, 03 Apr 2021 07:53:01: 16000000 INFO @ Sat, 03 Apr 2021 07:53:02: 12000000 INFO @ Sat, 03 Apr 2021 07:53:06: 9000000 INFO @ Sat, 03 Apr 2021 07:53:09: 17000000 INFO @ Sat, 03 Apr 2021 07:53:10: 13000000 INFO @ Sat, 03 Apr 2021 07:53:15: 10000000 INFO @ Sat, 03 Apr 2021 07:53:18: 18000000 INFO @ Sat, 03 Apr 2021 07:53:18: 14000000 INFO @ Sat, 03 Apr 2021 07:53:23: 11000000 INFO @ Sat, 03 Apr 2021 07:53:26: 19000000 INFO @ Sat, 03 Apr 2021 07:53:26: 15000000 INFO @ Sat, 03 Apr 2021 07:53:31: 12000000 INFO @ Sat, 03 Apr 2021 07:53:34: 16000000 INFO @ Sat, 03 Apr 2021 07:53:34: 20000000 INFO @ Sat, 03 Apr 2021 07:53:39: 13000000 INFO @ Sat, 03 Apr 2021 07:53:42: 17000000 INFO @ Sat, 03 Apr 2021 07:53:43: 21000000 INFO @ Sat, 03 Apr 2021 07:53:48: 14000000 INFO @ Sat, 03 Apr 2021 07:53:51: 18000000 INFO @ Sat, 03 Apr 2021 07:53:51: 22000000 INFO @ Sat, 03 Apr 2021 07:53:56: 15000000 INFO @ Sat, 03 Apr 2021 07:53:59: 19000000 INFO @ Sat, 03 Apr 2021 07:53:59: 23000000 INFO @ Sat, 03 Apr 2021 07:54:04: 16000000 INFO @ Sat, 03 Apr 2021 07:54:07: 20000000 INFO @ Sat, 03 Apr 2021 07:54:08: 24000000 INFO @ Sat, 03 Apr 2021 07:54:12: 17000000 INFO @ Sat, 03 Apr 2021 07:54:15: 21000000 INFO @ Sat, 03 Apr 2021 07:54:16: 25000000 INFO @ Sat, 03 Apr 2021 07:54:20: 18000000 INFO @ Sat, 03 Apr 2021 07:54:24: 22000000 INFO @ Sat, 03 Apr 2021 07:54:24: 26000000 INFO @ Sat, 03 Apr 2021 07:54:29: 19000000 INFO @ Sat, 03 Apr 2021 07:54:32: 23000000 INFO @ Sat, 03 Apr 2021 07:54:32: 27000000 INFO @ Sat, 03 Apr 2021 07:54:37: 20000000 INFO @ Sat, 03 Apr 2021 07:54:40: 24000000 INFO @ Sat, 03 Apr 2021 07:54:41: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:54:45: 21000000 INFO @ Sat, 03 Apr 2021 07:54:48: 25000000 INFO @ Sat, 03 Apr 2021 07:54:49: 29000000 INFO @ Sat, 03 Apr 2021 07:54:53: 22000000 INFO @ Sat, 03 Apr 2021 07:54:56: 26000000 INFO @ Sat, 03 Apr 2021 07:54:57: 30000000 INFO @ Sat, 03 Apr 2021 07:55:01: 23000000 INFO @ Sat, 03 Apr 2021 07:55:04: 27000000 INFO @ Sat, 03 Apr 2021 07:55:05: 31000000 INFO @ Sat, 03 Apr 2021 07:55:09: 24000000 INFO @ Sat, 03 Apr 2021 07:55:12: 28000000 INFO @ Sat, 03 Apr 2021 07:55:13: 32000000 INFO @ Sat, 03 Apr 2021 07:55:17: 25000000 INFO @ Sat, 03 Apr 2021 07:55:20: 29000000 INFO @ Sat, 03 Apr 2021 07:55:21: 33000000 INFO @ Sat, 03 Apr 2021 07:55:25: 26000000 INFO @ Sat, 03 Apr 2021 07:55:28: 30000000 INFO @ Sat, 03 Apr 2021 07:55:29: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 07:55:29: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 07:55:29: #1 total tags in treatment: 12910030 INFO @ Sat, 03 Apr 2021 07:55:29: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:55:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:55:29: #1 tags after filtering in treatment: 9320364 INFO @ Sat, 03 Apr 2021 07:55:29: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 03 Apr 2021 07:55:29: #1 finished! INFO @ Sat, 03 Apr 2021 07:55:29: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:55:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:55:29: #2 number of paired peaks: 210 WARNING @ Sat, 03 Apr 2021 07:55:29: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Sat, 03 Apr 2021 07:55:29: start model_add_line... INFO @ Sat, 03 Apr 2021 07:55:30: start X-correlation... INFO @ Sat, 03 Apr 2021 07:55:30: end of X-cor INFO @ Sat, 03 Apr 2021 07:55:30: #2 finished! INFO @ Sat, 03 Apr 2021 07:55:30: #2 predicted fragment length is 147 bps INFO @ Sat, 03 Apr 2021 07:55:30: #2 alternative fragment length(s) may be 4,129,147,161 bps INFO @ Sat, 03 Apr 2021 07:55:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.05_model.r WARNING @ Sat, 03 Apr 2021 07:55:30: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:55:30: #2 You may need to consider one of the other alternative d(s): 4,129,147,161 WARNING @ Sat, 03 Apr 2021 07:55:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:55:30: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:55:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:55:34: 27000000 INFO @ Sat, 03 Apr 2021 07:55:36: 31000000 INFO @ Sat, 03 Apr 2021 07:55:42: 28000000 INFO @ Sat, 03 Apr 2021 07:55:44: 32000000 INFO @ Sat, 03 Apr 2021 07:55:50: 29000000 INFO @ Sat, 03 Apr 2021 07:55:51: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:55:52: 33000000 INFO @ Sat, 03 Apr 2021 07:55:58: 30000000 INFO @ Sat, 03 Apr 2021 07:55:59: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 07:55:59: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 07:55:59: #1 total tags in treatment: 12910030 INFO @ Sat, 03 Apr 2021 07:55:59: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:55:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:55:59: #1 tags after filtering in treatment: 9320364 INFO @ Sat, 03 Apr 2021 07:55:59: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 03 Apr 2021 07:55:59: #1 finished! INFO @ Sat, 03 Apr 2021 07:55:59: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:55:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:56:00: #2 number of paired peaks: 210 WARNING @ Sat, 03 Apr 2021 07:56:00: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Sat, 03 Apr 2021 07:56:00: start model_add_line... INFO @ Sat, 03 Apr 2021 07:56:00: start X-correlation... INFO @ Sat, 03 Apr 2021 07:56:00: end of X-cor INFO @ Sat, 03 Apr 2021 07:56:00: #2 finished! INFO @ Sat, 03 Apr 2021 07:56:00: #2 predicted fragment length is 147 bps INFO @ Sat, 03 Apr 2021 07:56:00: #2 alternative fragment length(s) may be 4,129,147,161 bps INFO @ Sat, 03 Apr 2021 07:56:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.10_model.r WARNING @ Sat, 03 Apr 2021 07:56:00: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:56:00: #2 You may need to consider one of the other alternative d(s): 4,129,147,161 WARNING @ Sat, 03 Apr 2021 07:56:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:56:00: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:56:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:56:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:56:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:56:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.05_summits.bed INFO @ Sat, 03 Apr 2021 07:56:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (459 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:56:05: 31000000 INFO @ Sat, 03 Apr 2021 07:56:12: 32000000 INFO @ Sat, 03 Apr 2021 07:56:20: 33000000 INFO @ Sat, 03 Apr 2021 07:56:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:56:26: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 07:56:26: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 07:56:26: #1 total tags in treatment: 12910030 INFO @ Sat, 03 Apr 2021 07:56:26: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:56:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:56:27: #1 tags after filtering in treatment: 9320364 INFO @ Sat, 03 Apr 2021 07:56:27: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 03 Apr 2021 07:56:27: #1 finished! INFO @ Sat, 03 Apr 2021 07:56:27: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:56:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:56:27: #2 number of paired peaks: 210 WARNING @ Sat, 03 Apr 2021 07:56:27: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Sat, 03 Apr 2021 07:56:27: start model_add_line... INFO @ Sat, 03 Apr 2021 07:56:27: start X-correlation... INFO @ Sat, 03 Apr 2021 07:56:27: end of X-cor INFO @ Sat, 03 Apr 2021 07:56:27: #2 finished! INFO @ Sat, 03 Apr 2021 07:56:27: #2 predicted fragment length is 147 bps INFO @ Sat, 03 Apr 2021 07:56:27: #2 alternative fragment length(s) may be 4,129,147,161 bps INFO @ Sat, 03 Apr 2021 07:56:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.20_model.r WARNING @ Sat, 03 Apr 2021 07:56:27: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:56:27: #2 You may need to consider one of the other alternative d(s): 4,129,147,161 WARNING @ Sat, 03 Apr 2021 07:56:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:56:27: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:56:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:56:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:56:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:56:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.10_summits.bed INFO @ Sat, 03 Apr 2021 07:56:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (224 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:56:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:56:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:56:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:56:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2333001/SRX2333001.20_summits.bed INFO @ Sat, 03 Apr 2021 07:56:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (119 records, 4 fields): 1 millis CompletedMACS2peakCalling