Job ID = 8184513 SRX = SRX8047597 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T03:53:36 prefetch.2.10.7: 1) Downloading 'SRR11471321'... 2020-08-10T03:53:37 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T03:55:36 prefetch.2.10.7: HTTPS download succeed 2020-08-10T03:55:36 prefetch.2.10.7: 1) 'SRR11471321' was downloaded successfully Read 44951752 spots for SRR11471321/SRR11471321.sra Written 44951752 spots for SRR11471321/SRR11471321.sra 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: 00:49:28 44951752 reads; of these: 44951752 (100.00%) were unpaired; of these: 2787907 (6.20%) aligned 0 times 30523088 (67.90%) aligned exactly 1 time 11640757 (25.90%) aligned >1 times 93.80% overall alignment rate Time searching: 00:49:29 Overall time: 00:49:29 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 20 files... [bam_rmdupse_core] 5007928 / 42163845 = 0.1188 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 @ Mon, 10 Aug 2020 13:58:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.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 @ Mon, 10 Aug 2020 13:58:24: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:58:24: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:58:29: 1000000 INFO @ Mon, 10 Aug 2020 13:58:35: 2000000 INFO @ Mon, 10 Aug 2020 13:58:41: 3000000 INFO @ Mon, 10 Aug 2020 13:58:47: 4000000 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 @ Mon, 10 Aug 2020 13:58:53: 5000000 INFO @ Mon, 10 Aug 2020 13:58:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.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 @ Mon, 10 Aug 2020 13:58:54: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:58:54: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:58:59: 6000000 INFO @ Mon, 10 Aug 2020 13:59:00: 1000000 INFO @ Mon, 10 Aug 2020 13:59:06: 7000000 INFO @ Mon, 10 Aug 2020 13:59:07: 2000000 INFO @ Mon, 10 Aug 2020 13:59:12: 8000000 INFO @ Mon, 10 Aug 2020 13:59:13: 3000000 INFO @ Mon, 10 Aug 2020 13:59:19: 9000000 INFO @ Mon, 10 Aug 2020 13:59:20: 4000000 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 @ Mon, 10 Aug 2020 13:59:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.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 @ Mon, 10 Aug 2020 13:59:24: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:59:24: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:59:25: 10000000 INFO @ Mon, 10 Aug 2020 13:59:26: 5000000 INFO @ Mon, 10 Aug 2020 13:59:31: 1000000 INFO @ Mon, 10 Aug 2020 13:59:33: 11000000 INFO @ Mon, 10 Aug 2020 13:59:33: 6000000 INFO @ Mon, 10 Aug 2020 13:59:38: 2000000 INFO @ Mon, 10 Aug 2020 13:59:40: 12000000 INFO @ Mon, 10 Aug 2020 13:59:40: 7000000 INFO @ Mon, 10 Aug 2020 13:59:45: 3000000 INFO @ Mon, 10 Aug 2020 13:59:47: 13000000 INFO @ Mon, 10 Aug 2020 13:59:47: 8000000 INFO @ Mon, 10 Aug 2020 13:59:52: 4000000 INFO @ Mon, 10 Aug 2020 13:59:54: 14000000 INFO @ Mon, 10 Aug 2020 13:59:54: 9000000 INFO @ Mon, 10 Aug 2020 13:59:59: 5000000 INFO @ Mon, 10 Aug 2020 14:00:01: 15000000 INFO @ Mon, 10 Aug 2020 14:00:01: 10000000 INFO @ Mon, 10 Aug 2020 14:00:06: 6000000 INFO @ Mon, 10 Aug 2020 14:00:08: 16000000 INFO @ Mon, 10 Aug 2020 14:00:08: 11000000 INFO @ Mon, 10 Aug 2020 14:00:13: 7000000 INFO @ Mon, 10 Aug 2020 14:00:14: 17000000 INFO @ Mon, 10 Aug 2020 14:00:15: 12000000 INFO @ Mon, 10 Aug 2020 14:00:19: 8000000 INFO @ Mon, 10 Aug 2020 14:00:21: 18000000 INFO @ Mon, 10 Aug 2020 14:00:22: 13000000 INFO @ Mon, 10 Aug 2020 14:00:26: 9000000 INFO @ Mon, 10 Aug 2020 14:00:28: 19000000 INFO @ Mon, 10 Aug 2020 14:00:29: 14000000 INFO @ Mon, 10 Aug 2020 14:00:33: 10000000 INFO @ Mon, 10 Aug 2020 14:00:35: 20000000 INFO @ Mon, 10 Aug 2020 14:00:35: 15000000 INFO @ Mon, 10 Aug 2020 14:00:40: 11000000 INFO @ Mon, 10 Aug 2020 14:00:42: 21000000 INFO @ Mon, 10 Aug 2020 14:00:42: 16000000 INFO @ Mon, 10 Aug 2020 14:00:47: 12000000 INFO @ Mon, 10 Aug 2020 14:00:49: 22000000 INFO @ Mon, 10 Aug 2020 14:00:49: 17000000 INFO @ Mon, 10 Aug 2020 14:00:53: 13000000 INFO @ Mon, 10 Aug 2020 14:00:56: 23000000 INFO @ Mon, 10 Aug 2020 14:00:56: 18000000 INFO @ Mon, 10 Aug 2020 14:01:00: 14000000 INFO @ Mon, 10 Aug 2020 14:01:02: 24000000 INFO @ Mon, 10 Aug 2020 14:01:03: 19000000 INFO @ Mon, 10 Aug 2020 14:01:07: 15000000 INFO @ Mon, 10 Aug 2020 14:01:09: 25000000 INFO @ Mon, 10 Aug 2020 14:01:09: 20000000 INFO @ Mon, 10 Aug 2020 14:01:14: 16000000 INFO @ Mon, 10 Aug 2020 14:01:16: 26000000 INFO @ Mon, 10 Aug 2020 14:01:16: 21000000 INFO @ Mon, 10 Aug 2020 14:01:21: 17000000 INFO @ Mon, 10 Aug 2020 14:01:23: 27000000 INFO @ Mon, 10 Aug 2020 14:01:23: 22000000 INFO @ Mon, 10 Aug 2020 14:01:27: 18000000 INFO @ Mon, 10 Aug 2020 14:01:30: 28000000 INFO @ Mon, 10 Aug 2020 14:01:30: 23000000 INFO @ Mon, 10 Aug 2020 14:01:34: 19000000 INFO @ Mon, 10 Aug 2020 14:01:36: 29000000 INFO @ Mon, 10 Aug 2020 14:01:37: 24000000 INFO @ Mon, 10 Aug 2020 14:01:41: 20000000 INFO @ Mon, 10 Aug 2020 14:01:43: 30000000 INFO @ Mon, 10 Aug 2020 14:01:43: 25000000 INFO @ Mon, 10 Aug 2020 14:01:48: 21000000 INFO @ Mon, 10 Aug 2020 14:01:50: 31000000 INFO @ Mon, 10 Aug 2020 14:01:50: 26000000 INFO @ Mon, 10 Aug 2020 14:01:54: 22000000 INFO @ Mon, 10 Aug 2020 14:01:57: 32000000 INFO @ Mon, 10 Aug 2020 14:01:57: 27000000 INFO @ Mon, 10 Aug 2020 14:02:01: 23000000 INFO @ Mon, 10 Aug 2020 14:02:04: 33000000 INFO @ Mon, 10 Aug 2020 14:02:04: 28000000 INFO @ Mon, 10 Aug 2020 14:02:08: 24000000 INFO @ Mon, 10 Aug 2020 14:02:10: 29000000 INFO @ Mon, 10 Aug 2020 14:02:10: 34000000 INFO @ Mon, 10 Aug 2020 14:02:15: 25000000 INFO @ Mon, 10 Aug 2020 14:02:17: 30000000 INFO @ Mon, 10 Aug 2020 14:02:17: 35000000 INFO @ Mon, 10 Aug 2020 14:02:21: 26000000 INFO @ Mon, 10 Aug 2020 14:02:24: 31000000 INFO @ Mon, 10 Aug 2020 14:02:24: 36000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 14:02:28: 27000000 INFO @ Mon, 10 Aug 2020 14:02:31: 32000000 INFO @ Mon, 10 Aug 2020 14:02:31: 37000000 INFO @ Mon, 10 Aug 2020 14:02:32: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:02:32: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:02:32: #1 total tags in treatment: 37155917 INFO @ Mon, 10 Aug 2020 14:02:32: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:02:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 14:02:33: #1 tags after filtering in treatment: 37155844 INFO @ Mon, 10 Aug 2020 14:02:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:02:33: #1 finished! INFO @ Mon, 10 Aug 2020 14:02:33: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:02:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:02:35: 28000000 INFO @ Mon, 10 Aug 2020 14:02:36: #2 number of paired peaks: 8394 INFO @ Mon, 10 Aug 2020 14:02:36: start model_add_line... INFO @ Mon, 10 Aug 2020 14:02:36: start X-correlation... INFO @ Mon, 10 Aug 2020 14:02:36: end of X-cor INFO @ Mon, 10 Aug 2020 14:02:36: #2 finished! INFO @ Mon, 10 Aug 2020 14:02:36: #2 predicted fragment length is 55 bps INFO @ Mon, 10 Aug 2020 14:02:36: #2 alternative fragment length(s) may be 55 bps INFO @ Mon, 10 Aug 2020 14:02:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.05_model.r WARNING @ Mon, 10 Aug 2020 14:02:36: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:02:36: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Mon, 10 Aug 2020 14:02:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 14:02:36: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:02:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:02:37: 33000000 INFO @ Mon, 10 Aug 2020 14:02:41: 29000000 INFO @ Mon, 10 Aug 2020 14:02:44: 34000000 INFO @ Mon, 10 Aug 2020 14:02:48: 30000000 INFO @ Mon, 10 Aug 2020 14:02:50: 35000000 INFO @ Mon, 10 Aug 2020 14:02:55: 31000000 INFO @ Mon, 10 Aug 2020 14:02:57: 36000000 INFO @ Mon, 10 Aug 2020 14:03:01: 32000000 INFO @ Mon, 10 Aug 2020 14:03:04: 37000000 INFO @ Mon, 10 Aug 2020 14:03:05: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:03:05: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:03:05: #1 total tags in treatment: 37155917 INFO @ Mon, 10 Aug 2020 14:03:05: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:03:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 14:03:06: #1 tags after filtering in treatment: 37155844 INFO @ Mon, 10 Aug 2020 14:03:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:03:06: #1 finished! INFO @ Mon, 10 Aug 2020 14:03:06: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:03:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:03:08: 33000000 INFO @ Mon, 10 Aug 2020 14:03:09: #2 number of paired peaks: 8394 INFO @ Mon, 10 Aug 2020 14:03:09: start model_add_line... INFO @ Mon, 10 Aug 2020 14:03:09: start X-correlation... INFO @ Mon, 10 Aug 2020 14:03:09: end of X-cor INFO @ Mon, 10 Aug 2020 14:03:09: #2 finished! INFO @ Mon, 10 Aug 2020 14:03:09: #2 predicted fragment length is 55 bps INFO @ Mon, 10 Aug 2020 14:03:09: #2 alternative fragment length(s) may be 55 bps INFO @ Mon, 10 Aug 2020 14:03:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.10_model.r WARNING @ Mon, 10 Aug 2020 14:03:09: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:03:09: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Mon, 10 Aug 2020 14:03:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 14:03:09: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:03:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:03:14: 34000000 INFO @ Mon, 10 Aug 2020 14:03:20: 35000000 INFO @ Mon, 10 Aug 2020 14:03:26: 36000000 INFO @ Mon, 10 Aug 2020 14:03:32: 37000000 INFO @ Mon, 10 Aug 2020 14:03:33: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:03:33: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:03:33: #1 total tags in treatment: 37155917 INFO @ Mon, 10 Aug 2020 14:03:33: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:03:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 14:03:33: #1 tags after filtering in treatment: 37155844 INFO @ Mon, 10 Aug 2020 14:03:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:03:33: #1 finished! INFO @ Mon, 10 Aug 2020 14:03:33: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:03:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:03:37: #2 number of paired peaks: 8394 INFO @ Mon, 10 Aug 2020 14:03:37: start model_add_line... INFO @ Mon, 10 Aug 2020 14:03:37: start X-correlation... INFO @ Mon, 10 Aug 2020 14:03:37: end of X-cor INFO @ Mon, 10 Aug 2020 14:03:37: #2 finished! INFO @ Mon, 10 Aug 2020 14:03:37: #2 predicted fragment length is 55 bps INFO @ Mon, 10 Aug 2020 14:03:37: #2 alternative fragment length(s) may be 55 bps INFO @ Mon, 10 Aug 2020 14:03:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.20_model.r WARNING @ Mon, 10 Aug 2020 14:03:37: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:03:37: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Mon, 10 Aug 2020 14:03:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 14:03:37: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:03:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:03:54: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 14:04:27: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:04:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.05_peaks.xls INFO @ Mon, 10 Aug 2020 14:04:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:04:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.05_summits.bed INFO @ Mon, 10 Aug 2020 14:04:35: Done! pass1 - making usageList (82 chroms): 2 millis pass2 - checking and writing primary data (10061 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:04:54: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:05:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.10_peaks.xls INFO @ Mon, 10 Aug 2020 14:05:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:05:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.10_summits.bed INFO @ Mon, 10 Aug 2020 14:05:06: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (3335 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:05:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.20_peaks.xls INFO @ Mon, 10 Aug 2020 14:05:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:05:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047597/SRX8047597.20_summits.bed INFO @ Mon, 10 Aug 2020 14:05:33: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (924 records, 4 fields): 3 millis CompletedMACS2peakCalling