Job ID = 12265592 SRX = SRX7246271 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: 00:51:50 27744099 reads; of these: 27744099 (100.00%) were paired; of these: 15359250 (55.36%) aligned concordantly 0 times 10742858 (38.72%) aligned concordantly exactly 1 time 1641991 (5.92%) aligned concordantly >1 times ---- 15359250 pairs aligned concordantly 0 times; of these: 3440608 (22.40%) aligned discordantly 1 time ---- 11918642 pairs aligned 0 times concordantly or discordantly; of these: 23837284 mates make up the pairs; of these: 22336640 (93.70%) aligned 0 times 575462 (2.41%) aligned exactly 1 time 925182 (3.88%) aligned >1 times 59.75% overall alignment rate Time searching: 00:51:51 Overall time: 00:51:51 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 28 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] 6844124 / 15715636 = 0.4355 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 08:49:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.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 08:49:49: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:49:49: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:50:01: 1000000 INFO @ Sat, 03 Apr 2021 08:50:12: 2000000 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 08:50:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.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 08:50:19: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:50:19: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:50:25: 3000000 INFO @ Sat, 03 Apr 2021 08:50:32: 1000000 INFO @ Sat, 03 Apr 2021 08:50:37: 4000000 INFO @ Sat, 03 Apr 2021 08:50:45: 2000000 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 08:50:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.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 08:50:49: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:50:49: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:50:50: 5000000 INFO @ Sat, 03 Apr 2021 08:50:57: 3000000 INFO @ Sat, 03 Apr 2021 08:51:01: 1000000 INFO @ Sat, 03 Apr 2021 08:51:03: 6000000 INFO @ Sat, 03 Apr 2021 08:51:10: 4000000 INFO @ Sat, 03 Apr 2021 08:51:13: 2000000 INFO @ Sat, 03 Apr 2021 08:51:16: 7000000 INFO @ Sat, 03 Apr 2021 08:51:23: 5000000 INFO @ Sat, 03 Apr 2021 08:51:24: 3000000 INFO @ Sat, 03 Apr 2021 08:51:30: 8000000 INFO @ Sat, 03 Apr 2021 08:51:36: 4000000 INFO @ Sat, 03 Apr 2021 08:51:37: 6000000 INFO @ Sat, 03 Apr 2021 08:51:44: 9000000 INFO @ Sat, 03 Apr 2021 08:51:49: 5000000 INFO @ Sat, 03 Apr 2021 08:51:51: 7000000 INFO @ Sat, 03 Apr 2021 08:51:58: 10000000 INFO @ Sat, 03 Apr 2021 08:52:01: 6000000 INFO @ Sat, 03 Apr 2021 08:52:05: 8000000 INFO @ Sat, 03 Apr 2021 08:52:12: 11000000 INFO @ Sat, 03 Apr 2021 08:52:13: 7000000 INFO @ Sat, 03 Apr 2021 08:52:19: 9000000 INFO @ Sat, 03 Apr 2021 08:52:25: 8000000 INFO @ Sat, 03 Apr 2021 08:52:26: 12000000 INFO @ Sat, 03 Apr 2021 08:52:33: 10000000 INFO @ Sat, 03 Apr 2021 08:52:38: 9000000 INFO @ Sat, 03 Apr 2021 08:52:40: 13000000 INFO @ Sat, 03 Apr 2021 08:52:47: 11000000 INFO @ Sat, 03 Apr 2021 08:52:50: 10000000 INFO @ Sat, 03 Apr 2021 08:52:53: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:53:01: 12000000 INFO @ Sat, 03 Apr 2021 08:53:02: 11000000 INFO @ Sat, 03 Apr 2021 08:53:07: 15000000 INFO @ Sat, 03 Apr 2021 08:53:14: 12000000 INFO @ Sat, 03 Apr 2021 08:53:14: 13000000 INFO @ Sat, 03 Apr 2021 08:53:21: 16000000 INFO @ Sat, 03 Apr 2021 08:53:26: 13000000 INFO @ Sat, 03 Apr 2021 08:53:28: 14000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:53:35: 17000000 INFO @ Sat, 03 Apr 2021 08:53:38: 14000000 INFO @ Sat, 03 Apr 2021 08:53:42: 15000000 INFO @ Sat, 03 Apr 2021 08:53:49: 18000000 INFO @ Sat, 03 Apr 2021 08:53:51: 15000000 INFO @ Sat, 03 Apr 2021 08:53:56: 16000000 INFO @ Sat, 03 Apr 2021 08:54:02: 19000000 INFO @ Sat, 03 Apr 2021 08:54:04: 16000000 INFO @ Sat, 03 Apr 2021 08:54:08: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 08:54:08: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 08:54:08: #1 total tags in treatment: 6868379 INFO @ Sat, 03 Apr 2021 08:54:08: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:54:08: #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 08:54:08: #1 tags after filtering in treatment: 4856746 INFO @ Sat, 03 Apr 2021 08:54:08: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 03 Apr 2021 08:54:08: #1 finished! INFO @ Sat, 03 Apr 2021 08:54:08: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:54:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:54:09: #2 number of paired peaks: 1512 INFO @ Sat, 03 Apr 2021 08:54:09: start model_add_line... INFO @ Sat, 03 Apr 2021 08:54:09: start X-correlation... INFO @ Sat, 03 Apr 2021 08:54:09: end of X-cor INFO @ Sat, 03 Apr 2021 08:54:09: #2 finished! INFO @ Sat, 03 Apr 2021 08:54:09: #2 predicted fragment length is 189 bps INFO @ Sat, 03 Apr 2021 08:54:09: #2 alternative fragment length(s) may be 189 bps INFO @ Sat, 03 Apr 2021 08:54:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.05_model.r WARNING @ Sat, 03 Apr 2021 08:54:09: #2 Since the d (189) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:54:09: #2 You may need to consider one of the other alternative d(s): 189 WARNING @ Sat, 03 Apr 2021 08:54:09: #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 08:54:09: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:54:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:54:09: 17000000 INFO @ Sat, 03 Apr 2021 08:54:16: 17000000 INFO @ Sat, 03 Apr 2021 08:54:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:54:22: 18000000 INFO @ Sat, 03 Apr 2021 08:54:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:54:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:54:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.05_summits.bed INFO @ Sat, 03 Apr 2021 08:54:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3509 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:54:29: 18000000 INFO @ Sat, 03 Apr 2021 08:54:34: 19000000 INFO @ Sat, 03 Apr 2021 08:54:39: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 08:54:39: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 08:54:39: #1 total tags in treatment: 6868379 INFO @ Sat, 03 Apr 2021 08:54:39: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:54:39: #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 08:54:39: #1 tags after filtering in treatment: 4856746 INFO @ Sat, 03 Apr 2021 08:54:39: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 03 Apr 2021 08:54:39: #1 finished! INFO @ Sat, 03 Apr 2021 08:54:39: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:54:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:54:40: #2 number of paired peaks: 1512 INFO @ Sat, 03 Apr 2021 08:54:40: start model_add_line... INFO @ Sat, 03 Apr 2021 08:54:40: start X-correlation... INFO @ Sat, 03 Apr 2021 08:54:40: end of X-cor INFO @ Sat, 03 Apr 2021 08:54:40: #2 finished! INFO @ Sat, 03 Apr 2021 08:54:40: #2 predicted fragment length is 189 bps INFO @ Sat, 03 Apr 2021 08:54:40: #2 alternative fragment length(s) may be 189 bps INFO @ Sat, 03 Apr 2021 08:54:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.10_model.r WARNING @ Sat, 03 Apr 2021 08:54:40: #2 Since the d (189) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:54:40: #2 You may need to consider one of the other alternative d(s): 189 WARNING @ Sat, 03 Apr 2021 08:54:40: #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 08:54:40: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:54:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:54:41: 19000000 INFO @ Sat, 03 Apr 2021 08:54:46: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 08:54:46: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 08:54:46: #1 total tags in treatment: 6868379 INFO @ Sat, 03 Apr 2021 08:54:46: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:54:46: #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 08:54:46: #1 tags after filtering in treatment: 4856746 INFO @ Sat, 03 Apr 2021 08:54:46: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 03 Apr 2021 08:54:46: #1 finished! INFO @ Sat, 03 Apr 2021 08:54:46: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:54:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:54:47: #2 number of paired peaks: 1512 INFO @ Sat, 03 Apr 2021 08:54:47: start model_add_line... INFO @ Sat, 03 Apr 2021 08:54:47: start X-correlation... INFO @ Sat, 03 Apr 2021 08:54:47: end of X-cor INFO @ Sat, 03 Apr 2021 08:54:47: #2 finished! INFO @ Sat, 03 Apr 2021 08:54:47: #2 predicted fragment length is 189 bps INFO @ Sat, 03 Apr 2021 08:54:47: #2 alternative fragment length(s) may be 189 bps INFO @ Sat, 03 Apr 2021 08:54:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.20_model.r WARNING @ Sat, 03 Apr 2021 08:54:47: #2 Since the d (189) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:54:47: #2 You may need to consider one of the other alternative d(s): 189 WARNING @ Sat, 03 Apr 2021 08:54:47: #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 08:54:47: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:54:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:54:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:54:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:54:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:54:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.10_summits.bed INFO @ Sat, 03 Apr 2021 08:54:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2173 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:54:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:55:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:55:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:55:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246271/SRX7246271.20_summits.bed INFO @ Sat, 03 Apr 2021 08:55:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1175 records, 4 fields): 3 millis CompletedMACS2peakCalling