Job ID = 7096652 SRX = SRX3919490 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 54971730 spots for SRR6978718/SRR6978718.sra Written 54971730 spots for SRR6978718/SRR6978718.sra 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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:23:51 54971730 reads; of these: 54971730 (100.00%) were unpaired; of these: 21685233 (39.45%) aligned 0 times 24947316 (45.38%) aligned exactly 1 time 8339181 (15.17%) aligned >1 times 60.55% overall alignment rate Time searching: 00:23:55 Overall time: 00:23:55 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 1648575 / 33286497 = 0.0495 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 11:33:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Jul 2020 11:33:18: #1 read tag files... INFO @ Wed, 22 Jul 2020 11:33:18: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 11:33:22: 1000000 INFO @ Wed, 22 Jul 2020 11:33:27: 2000000 INFO @ Wed, 22 Jul 2020 11:33:32: 3000000 INFO @ Wed, 22 Jul 2020 11:33:36: 4000000 INFO @ Wed, 22 Jul 2020 11:33:41: 5000000 INFO @ Wed, 22 Jul 2020 11:33:46: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 11:33:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Jul 2020 11:33:48: #1 read tag files... INFO @ Wed, 22 Jul 2020 11:33:48: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 11:33:50: 7000000 INFO @ Wed, 22 Jul 2020 11:33:52: 1000000 INFO @ Wed, 22 Jul 2020 11:33:55: 8000000 INFO @ Wed, 22 Jul 2020 11:33:57: 2000000 INFO @ Wed, 22 Jul 2020 11:33:59: 9000000 INFO @ Wed, 22 Jul 2020 11:34:01: 3000000 INFO @ Wed, 22 Jul 2020 11:34:04: 10000000 INFO @ Wed, 22 Jul 2020 11:34:06: 4000000 INFO @ Wed, 22 Jul 2020 11:34:09: 11000000 INFO @ Wed, 22 Jul 2020 11:34:11: 5000000 INFO @ Wed, 22 Jul 2020 11:34:13: 12000000 INFO @ Wed, 22 Jul 2020 11:34:16: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 11:34:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Jul 2020 11:34:18: #1 read tag files... INFO @ Wed, 22 Jul 2020 11:34:18: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 11:34:18: 13000000 INFO @ Wed, 22 Jul 2020 11:34:20: 7000000 INFO @ Wed, 22 Jul 2020 11:34:23: 1000000 INFO @ Wed, 22 Jul 2020 11:34:23: 14000000 INFO @ Wed, 22 Jul 2020 11:34:25: 8000000 INFO @ Wed, 22 Jul 2020 11:34:27: 2000000 INFO @ Wed, 22 Jul 2020 11:34:27: 15000000 INFO @ Wed, 22 Jul 2020 11:34:30: 9000000 INFO @ Wed, 22 Jul 2020 11:34:32: 16000000 INFO @ Wed, 22 Jul 2020 11:34:32: 3000000 INFO @ Wed, 22 Jul 2020 11:34:34: 10000000 INFO @ Wed, 22 Jul 2020 11:34:37: 17000000 INFO @ Wed, 22 Jul 2020 11:34:37: 4000000 INFO @ Wed, 22 Jul 2020 11:34:39: 11000000 INFO @ Wed, 22 Jul 2020 11:34:42: 18000000 INFO @ Wed, 22 Jul 2020 11:34:42: 5000000 INFO @ Wed, 22 Jul 2020 11:34:44: 12000000 INFO @ Wed, 22 Jul 2020 11:34:46: 19000000 INFO @ Wed, 22 Jul 2020 11:34:47: 6000000 INFO @ Wed, 22 Jul 2020 11:34:48: 13000000 INFO @ Wed, 22 Jul 2020 11:34:51: 20000000 INFO @ Wed, 22 Jul 2020 11:34:52: 7000000 INFO @ Wed, 22 Jul 2020 11:34:53: 14000000 INFO @ Wed, 22 Jul 2020 11:34:56: 21000000 INFO @ Wed, 22 Jul 2020 11:34:56: 8000000 INFO @ Wed, 22 Jul 2020 11:34:57: 15000000 INFO @ Wed, 22 Jul 2020 11:35:01: 22000000 INFO @ Wed, 22 Jul 2020 11:35:01: 9000000 INFO @ Wed, 22 Jul 2020 11:35:02: 16000000 INFO @ Wed, 22 Jul 2020 11:35:05: 23000000 INFO @ Wed, 22 Jul 2020 11:35:06: 10000000 INFO @ Wed, 22 Jul 2020 11:35:07: 17000000 INFO @ Wed, 22 Jul 2020 11:35:10: 24000000 INFO @ Wed, 22 Jul 2020 11:35:10: 11000000 INFO @ Wed, 22 Jul 2020 11:35:11: 18000000 INFO @ Wed, 22 Jul 2020 11:35:15: 25000000 INFO @ Wed, 22 Jul 2020 11:35:15: 12000000 INFO @ Wed, 22 Jul 2020 11:35:16: 19000000 INFO @ Wed, 22 Jul 2020 11:35:19: 26000000 INFO @ Wed, 22 Jul 2020 11:35:20: 13000000 INFO @ Wed, 22 Jul 2020 11:35:21: 20000000 INFO @ Wed, 22 Jul 2020 11:35:24: 27000000 INFO @ Wed, 22 Jul 2020 11:35:25: 14000000 INFO @ Wed, 22 Jul 2020 11:35:25: 21000000 INFO @ Wed, 22 Jul 2020 11:35:29: 28000000 INFO @ Wed, 22 Jul 2020 11:35:30: 15000000 INFO @ Wed, 22 Jul 2020 11:35:30: 22000000 INFO @ Wed, 22 Jul 2020 11:35:33: 29000000 INFO @ Wed, 22 Jul 2020 11:35:34: 16000000 INFO @ Wed, 22 Jul 2020 11:35:34: 23000000 INFO @ Wed, 22 Jul 2020 11:35:38: 30000000 INFO @ Wed, 22 Jul 2020 11:35:39: 17000000 INFO @ Wed, 22 Jul 2020 11:35:39: 24000000 INFO @ Wed, 22 Jul 2020 11:35:43: 31000000 INFO @ Wed, 22 Jul 2020 11:35:44: 25000000 INFO @ Wed, 22 Jul 2020 11:35:44: 18000000 INFO @ Wed, 22 Jul 2020 11:35:46: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 11:35:46: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 11:35:46: #1 total tags in treatment: 31637922 INFO @ Wed, 22 Jul 2020 11:35:46: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 11:35:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 11:35:47: #1 tags after filtering in treatment: 31637795 INFO @ Wed, 22 Jul 2020 11:35:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 11:35:47: #1 finished! INFO @ Wed, 22 Jul 2020 11:35:47: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 11:35:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 11:35:48: 26000000 INFO @ Wed, 22 Jul 2020 11:35:48: 19000000 INFO @ Wed, 22 Jul 2020 11:35:49: #2 number of paired peaks: 3624 INFO @ Wed, 22 Jul 2020 11:35:49: start model_add_line... INFO @ Wed, 22 Jul 2020 11:35:50: start X-correlation... INFO @ Wed, 22 Jul 2020 11:35:50: end of X-cor INFO @ Wed, 22 Jul 2020 11:35:50: #2 finished! INFO @ Wed, 22 Jul 2020 11:35:50: #2 predicted fragment length is 49 bps INFO @ Wed, 22 Jul 2020 11:35:50: #2 alternative fragment length(s) may be 49,410,513 bps INFO @ Wed, 22 Jul 2020 11:35:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.05_model.r WARNING @ Wed, 22 Jul 2020 11:35:50: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 11:35:50: #2 You may need to consider one of the other alternative d(s): 49,410,513 WARNING @ Wed, 22 Jul 2020 11:35:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 11:35:50: #3 Call peaks... INFO @ Wed, 22 Jul 2020 11:35:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 11:35:53: 27000000 INFO @ Wed, 22 Jul 2020 11:35:53: 20000000 INFO @ Wed, 22 Jul 2020 11:35:57: 28000000 INFO @ Wed, 22 Jul 2020 11:35:58: 21000000 INFO @ Wed, 22 Jul 2020 11:36:02: 29000000 INFO @ Wed, 22 Jul 2020 11:36:02: 22000000 INFO @ Wed, 22 Jul 2020 11:36:06: 30000000 INFO @ Wed, 22 Jul 2020 11:36:07: 23000000 INFO @ Wed, 22 Jul 2020 11:36:11: 31000000 INFO @ Wed, 22 Jul 2020 11:36:12: 24000000 INFO @ Wed, 22 Jul 2020 11:36:14: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 11:36:14: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 11:36:14: #1 total tags in treatment: 31637922 INFO @ Wed, 22 Jul 2020 11:36:14: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 11:36:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 11:36:15: #1 tags after filtering in treatment: 31637795 INFO @ Wed, 22 Jul 2020 11:36:15: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 11:36:15: #1 finished! INFO @ Wed, 22 Jul 2020 11:36:15: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 11:36:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 11:36:16: 25000000 INFO @ Wed, 22 Jul 2020 11:36:18: #2 number of paired peaks: 3624 INFO @ Wed, 22 Jul 2020 11:36:18: start model_add_line... INFO @ Wed, 22 Jul 2020 11:36:18: start X-correlation... INFO @ Wed, 22 Jul 2020 11:36:18: end of X-cor INFO @ Wed, 22 Jul 2020 11:36:18: #2 finished! INFO @ Wed, 22 Jul 2020 11:36:18: #2 predicted fragment length is 49 bps INFO @ Wed, 22 Jul 2020 11:36:18: #2 alternative fragment length(s) may be 49,410,513 bps INFO @ Wed, 22 Jul 2020 11:36:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.10_model.r WARNING @ Wed, 22 Jul 2020 11:36:18: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 11:36:18: #2 You may need to consider one of the other alternative d(s): 49,410,513 WARNING @ Wed, 22 Jul 2020 11:36:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 11:36:18: #3 Call peaks... INFO @ Wed, 22 Jul 2020 11:36:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 11:36:21: 26000000 INFO @ Wed, 22 Jul 2020 11:36:26: 27000000 INFO @ Wed, 22 Jul 2020 11:36:30: 28000000 INFO @ Wed, 22 Jul 2020 11:36:35: 29000000 INFO @ Wed, 22 Jul 2020 11:36:39: 30000000 INFO @ Wed, 22 Jul 2020 11:36:44: 31000000 INFO @ Wed, 22 Jul 2020 11:36:47: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 11:36:47: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 11:36:47: #1 total tags in treatment: 31637922 INFO @ Wed, 22 Jul 2020 11:36:47: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 11:36:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 11:36:48: #1 tags after filtering in treatment: 31637795 INFO @ Wed, 22 Jul 2020 11:36:48: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 11:36:48: #1 finished! INFO @ Wed, 22 Jul 2020 11:36:48: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 11:36:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 11:36:50: #2 number of paired peaks: 3624 INFO @ Wed, 22 Jul 2020 11:36:50: start model_add_line... INFO @ Wed, 22 Jul 2020 11:36:51: start X-correlation... INFO @ Wed, 22 Jul 2020 11:36:51: end of X-cor INFO @ Wed, 22 Jul 2020 11:36:51: #2 finished! INFO @ Wed, 22 Jul 2020 11:36:51: #2 predicted fragment length is 49 bps INFO @ Wed, 22 Jul 2020 11:36:51: #2 alternative fragment length(s) may be 49,410,513 bps INFO @ Wed, 22 Jul 2020 11:36:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.20_model.r WARNING @ Wed, 22 Jul 2020 11:36:51: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 11:36:51: #2 You may need to consider one of the other alternative d(s): 49,410,513 WARNING @ Wed, 22 Jul 2020 11:36:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 11:36:51: #3 Call peaks... INFO @ Wed, 22 Jul 2020 11:36:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 11:36:58: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 11:37:26: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 11:37:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.05_peaks.xls INFO @ Wed, 22 Jul 2020 11:37:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 11:37:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.05_summits.bed INFO @ Wed, 22 Jul 2020 11:37:33: Done! pass1 - making usageList (67 chroms): 1 millis pass2 - checking and writing primary data (1952 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 11:37:57: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 11:38:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.10_peaks.xls INFO @ Wed, 22 Jul 2020 11:38:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 11:38:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.10_summits.bed INFO @ Wed, 22 Jul 2020 11:38:01: Done! pass1 - making usageList (62 chroms): 1 millis pass2 - checking and writing primary data (1139 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 11:38:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.20_peaks.xls INFO @ Wed, 22 Jul 2020 11:38:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 11:38:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3919490/SRX3919490.20_summits.bed INFO @ Wed, 22 Jul 2020 11:38:33: Done! pass1 - making usageList (53 chroms): 1 millis pass2 - checking and writing primary data (552 records, 4 fields): 3 millis CompletedMACS2peakCalling