Job ID = 7096702 SRX = SRX3919491 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 65573038 spots for SRR6978719/SRR6978719.sra Written 65573038 spots for SRR6978719/SRR6978719.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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:35:10 65573038 reads; of these: 65573038 (100.00%) were unpaired; of these: 20290463 (30.94%) aligned 0 times 33916516 (51.72%) aligned exactly 1 time 11366059 (17.33%) aligned >1 times 69.06% overall alignment rate Time searching: 00:35:12 Overall time: 00:35:12 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] 2652936 / 45282575 = 0.0586 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 11:49:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.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 11:49:16: #1 read tag files... INFO @ Wed, 22 Jul 2020 11:49:16: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 11:49:22: 1000000 INFO @ Wed, 22 Jul 2020 11:49:27: 2000000 INFO @ Wed, 22 Jul 2020 11:49:32: 3000000 INFO @ Wed, 22 Jul 2020 11:49:37: 4000000 INFO @ Wed, 22 Jul 2020 11:49:42: 5000000 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 11:49:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.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 11:49:46: #1 read tag files... INFO @ Wed, 22 Jul 2020 11:49:46: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 11:49:48: 6000000 INFO @ Wed, 22 Jul 2020 11:49:52: 1000000 INFO @ Wed, 22 Jul 2020 11:49:53: 7000000 INFO @ Wed, 22 Jul 2020 11:49:57: 2000000 INFO @ Wed, 22 Jul 2020 11:49:58: 8000000 INFO @ Wed, 22 Jul 2020 11:50:03: 3000000 INFO @ Wed, 22 Jul 2020 11:50:04: 9000000 INFO @ Wed, 22 Jul 2020 11:50:08: 4000000 INFO @ Wed, 22 Jul 2020 11:50:09: 10000000 INFO @ Wed, 22 Jul 2020 11:50:13: 5000000 INFO @ Wed, 22 Jul 2020 11:50:14: 11000000 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 11:50:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.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 11:50:16: #1 read tag files... INFO @ Wed, 22 Jul 2020 11:50:16: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 11:50:19: 6000000 INFO @ Wed, 22 Jul 2020 11:50:20: 12000000 INFO @ Wed, 22 Jul 2020 11:50:22: 1000000 INFO @ Wed, 22 Jul 2020 11:50:24: 7000000 INFO @ Wed, 22 Jul 2020 11:50:26: 13000000 INFO @ Wed, 22 Jul 2020 11:50:28: 2000000 INFO @ Wed, 22 Jul 2020 11:50:30: 8000000 INFO @ Wed, 22 Jul 2020 11:50:31: 14000000 INFO @ Wed, 22 Jul 2020 11:50:33: 3000000 INFO @ Wed, 22 Jul 2020 11:50:35: 9000000 INFO @ Wed, 22 Jul 2020 11:50:37: 15000000 INFO @ Wed, 22 Jul 2020 11:50:39: 4000000 INFO @ Wed, 22 Jul 2020 11:50:41: 10000000 INFO @ Wed, 22 Jul 2020 11:50:42: 16000000 INFO @ Wed, 22 Jul 2020 11:50:44: 5000000 INFO @ Wed, 22 Jul 2020 11:50:46: 11000000 INFO @ Wed, 22 Jul 2020 11:50:48: 17000000 INFO @ Wed, 22 Jul 2020 11:50:50: 6000000 INFO @ Wed, 22 Jul 2020 11:50:51: 12000000 INFO @ Wed, 22 Jul 2020 11:50:53: 18000000 INFO @ Wed, 22 Jul 2020 11:50:55: 7000000 INFO @ Wed, 22 Jul 2020 11:50:57: 13000000 INFO @ Wed, 22 Jul 2020 11:50:59: 19000000 INFO @ Wed, 22 Jul 2020 11:51:00: 8000000 INFO @ Wed, 22 Jul 2020 11:51:02: 14000000 INFO @ Wed, 22 Jul 2020 11:51:04: 20000000 INFO @ Wed, 22 Jul 2020 11:51:06: 9000000 INFO @ Wed, 22 Jul 2020 11:51:08: 15000000 INFO @ Wed, 22 Jul 2020 11:51:09: 21000000 INFO @ Wed, 22 Jul 2020 11:51:11: 10000000 INFO @ Wed, 22 Jul 2020 11:51:13: 16000000 INFO @ Wed, 22 Jul 2020 11:51:15: 22000000 INFO @ Wed, 22 Jul 2020 11:51:17: 11000000 INFO @ Wed, 22 Jul 2020 11:51:18: 17000000 INFO @ Wed, 22 Jul 2020 11:51:20: 23000000 INFO @ Wed, 22 Jul 2020 11:51:22: 12000000 INFO @ Wed, 22 Jul 2020 11:51:24: 18000000 INFO @ Wed, 22 Jul 2020 11:51:25: 24000000 INFO @ Wed, 22 Jul 2020 11:51:28: 13000000 INFO @ Wed, 22 Jul 2020 11:51:29: 19000000 INFO @ Wed, 22 Jul 2020 11:51:31: 25000000 INFO @ Wed, 22 Jul 2020 11:51:33: 14000000 INFO @ Wed, 22 Jul 2020 11:51:35: 20000000 INFO @ Wed, 22 Jul 2020 11:51:36: 26000000 INFO @ Wed, 22 Jul 2020 11:51:39: 15000000 INFO @ Wed, 22 Jul 2020 11:51:40: 21000000 INFO @ Wed, 22 Jul 2020 11:51:41: 27000000 INFO @ Wed, 22 Jul 2020 11:51:44: 16000000 INFO @ Wed, 22 Jul 2020 11:51:45: 22000000 INFO @ Wed, 22 Jul 2020 11:51:47: 28000000 INFO @ Wed, 22 Jul 2020 11:51:50: 17000000 INFO @ Wed, 22 Jul 2020 11:51:51: 23000000 INFO @ Wed, 22 Jul 2020 11:51:52: 29000000 INFO @ Wed, 22 Jul 2020 11:51:55: 18000000 INFO @ Wed, 22 Jul 2020 11:51:56: 24000000 INFO @ Wed, 22 Jul 2020 11:51:57: 30000000 INFO @ Wed, 22 Jul 2020 11:52:01: 19000000 INFO @ Wed, 22 Jul 2020 11:52:02: 25000000 INFO @ Wed, 22 Jul 2020 11:52:02: 31000000 INFO @ Wed, 22 Jul 2020 11:52:06: 20000000 INFO @ Wed, 22 Jul 2020 11:52:07: 26000000 INFO @ Wed, 22 Jul 2020 11:52:08: 32000000 INFO @ Wed, 22 Jul 2020 11:52:11: 21000000 INFO @ Wed, 22 Jul 2020 11:52:12: 27000000 INFO @ Wed, 22 Jul 2020 11:52:13: 33000000 INFO @ Wed, 22 Jul 2020 11:52:17: 22000000 INFO @ Wed, 22 Jul 2020 11:52:17: 28000000 INFO @ Wed, 22 Jul 2020 11:52:18: 34000000 INFO @ Wed, 22 Jul 2020 11:52:22: 23000000 INFO @ Wed, 22 Jul 2020 11:52:23: 29000000 INFO @ Wed, 22 Jul 2020 11:52:23: 35000000 INFO @ Wed, 22 Jul 2020 11:52:28: 24000000 INFO @ Wed, 22 Jul 2020 11:52:28: 30000000 INFO @ Wed, 22 Jul 2020 11:52:29: 36000000 INFO @ Wed, 22 Jul 2020 11:52:33: 25000000 INFO @ Wed, 22 Jul 2020 11:52:33: 31000000 INFO @ Wed, 22 Jul 2020 11:52:34: 37000000 INFO @ Wed, 22 Jul 2020 11:52:39: 32000000 INFO @ Wed, 22 Jul 2020 11:52:39: 26000000 INFO @ Wed, 22 Jul 2020 11:52:39: 38000000 INFO @ Wed, 22 Jul 2020 11:52:44: 33000000 INFO @ Wed, 22 Jul 2020 11:52:44: 27000000 INFO @ Wed, 22 Jul 2020 11:52:44: 39000000 INFO @ Wed, 22 Jul 2020 11:52:49: 34000000 INFO @ Wed, 22 Jul 2020 11:52:49: 28000000 INFO @ Wed, 22 Jul 2020 11:52:50: 40000000 INFO @ Wed, 22 Jul 2020 11:52:54: 35000000 INFO @ Wed, 22 Jul 2020 11:52:55: 29000000 INFO @ Wed, 22 Jul 2020 11:52:55: 41000000 INFO @ Wed, 22 Jul 2020 11:53:00: 36000000 INFO @ Wed, 22 Jul 2020 11:53:00: 30000000 INFO @ Wed, 22 Jul 2020 11:53:00: 42000000 INFO @ Wed, 22 Jul 2020 11:53:04: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 11:53:04: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 11:53:04: #1 total tags in treatment: 42629639 INFO @ Wed, 22 Jul 2020 11:53:04: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 11:53:04: #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 11:53:05: #1 tags after filtering in treatment: 42629564 INFO @ Wed, 22 Jul 2020 11:53:05: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 11:53:05: #1 finished! INFO @ Wed, 22 Jul 2020 11:53:05: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 11:53:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 11:53:05: 37000000 INFO @ Wed, 22 Jul 2020 11:53:05: 31000000 INFO @ Wed, 22 Jul 2020 11:53:09: #2 number of paired peaks: 3633 INFO @ Wed, 22 Jul 2020 11:53:09: start model_add_line... INFO @ Wed, 22 Jul 2020 11:53:09: start X-correlation... INFO @ Wed, 22 Jul 2020 11:53:09: end of X-cor INFO @ Wed, 22 Jul 2020 11:53:09: #2 finished! INFO @ Wed, 22 Jul 2020 11:53:09: #2 predicted fragment length is 50 bps INFO @ Wed, 22 Jul 2020 11:53:09: #2 alternative fragment length(s) may be 50,401,527 bps INFO @ Wed, 22 Jul 2020 11:53:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.05_model.r WARNING @ Wed, 22 Jul 2020 11:53:09: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 11:53:09: #2 You may need to consider one of the other alternative d(s): 50,401,527 WARNING @ Wed, 22 Jul 2020 11:53:09: #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 11:53:09: #3 Call peaks... INFO @ Wed, 22 Jul 2020 11:53:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 11:53:10: 38000000 INFO @ Wed, 22 Jul 2020 11:53:11: 32000000 INFO @ Wed, 22 Jul 2020 11:53:16: 39000000 INFO @ Wed, 22 Jul 2020 11:53:16: 33000000 INFO @ Wed, 22 Jul 2020 11:53:21: 40000000 INFO @ Wed, 22 Jul 2020 11:53:21: 34000000 INFO @ Wed, 22 Jul 2020 11:53:26: 41000000 INFO @ Wed, 22 Jul 2020 11:53:27: 35000000 INFO @ Wed, 22 Jul 2020 11:53:32: 42000000 INFO @ Wed, 22 Jul 2020 11:53:32: 36000000 INFO @ Wed, 22 Jul 2020 11:53:35: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 11:53:35: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 11:53:35: #1 total tags in treatment: 42629639 INFO @ Wed, 22 Jul 2020 11:53:35: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 11:53:35: #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 11:53:36: #1 tags after filtering in treatment: 42629564 INFO @ Wed, 22 Jul 2020 11:53:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 11:53:36: #1 finished! INFO @ Wed, 22 Jul 2020 11:53:36: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 11:53:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 11:53:37: 37000000 INFO @ Wed, 22 Jul 2020 11:53:40: #2 number of paired peaks: 3633 INFO @ Wed, 22 Jul 2020 11:53:40: start model_add_line... INFO @ Wed, 22 Jul 2020 11:53:40: start X-correlation... INFO @ Wed, 22 Jul 2020 11:53:40: end of X-cor INFO @ Wed, 22 Jul 2020 11:53:40: #2 finished! INFO @ Wed, 22 Jul 2020 11:53:40: #2 predicted fragment length is 50 bps INFO @ Wed, 22 Jul 2020 11:53:40: #2 alternative fragment length(s) may be 50,401,527 bps INFO @ Wed, 22 Jul 2020 11:53:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.10_model.r WARNING @ Wed, 22 Jul 2020 11:53:40: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 11:53:40: #2 You may need to consider one of the other alternative d(s): 50,401,527 WARNING @ Wed, 22 Jul 2020 11:53:40: #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 11:53:40: #3 Call peaks... INFO @ Wed, 22 Jul 2020 11:53:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 11:53:42: 38000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 11:53:47: 39000000 INFO @ Wed, 22 Jul 2020 11:53:52: 40000000 INFO @ Wed, 22 Jul 2020 11:53:58: 41000000 INFO @ Wed, 22 Jul 2020 11:54:03: 42000000 INFO @ Wed, 22 Jul 2020 11:54:06: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 11:54:06: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 11:54:06: #1 total tags in treatment: 42629639 INFO @ Wed, 22 Jul 2020 11:54:06: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 11:54:06: #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 11:54:07: #1 tags after filtering in treatment: 42629564 INFO @ Wed, 22 Jul 2020 11:54:07: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 11:54:07: #1 finished! INFO @ Wed, 22 Jul 2020 11:54:07: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 11:54:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 11:54:11: #2 number of paired peaks: 3633 INFO @ Wed, 22 Jul 2020 11:54:11: start model_add_line... INFO @ Wed, 22 Jul 2020 11:54:11: start X-correlation... INFO @ Wed, 22 Jul 2020 11:54:11: end of X-cor INFO @ Wed, 22 Jul 2020 11:54:11: #2 finished! INFO @ Wed, 22 Jul 2020 11:54:11: #2 predicted fragment length is 50 bps INFO @ Wed, 22 Jul 2020 11:54:11: #2 alternative fragment length(s) may be 50,401,527 bps INFO @ Wed, 22 Jul 2020 11:54:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.20_model.r WARNING @ Wed, 22 Jul 2020 11:54:11: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 11:54:11: #2 You may need to consider one of the other alternative d(s): 50,401,527 WARNING @ Wed, 22 Jul 2020 11:54:11: #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 11:54:11: #3 Call peaks... INFO @ Wed, 22 Jul 2020 11:54:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 11:54:44: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 11:55:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 11:55:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.05_peaks.xls INFO @ Wed, 22 Jul 2020 11:55:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 11:55:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.05_summits.bed INFO @ Wed, 22 Jul 2020 11:55:35: Done! pass1 - making usageList (68 chroms): 1 millis pass2 - checking and writing primary data (2305 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 11:55:46: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 11:56:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.10_peaks.xls INFO @ Wed, 22 Jul 2020 11:56:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 11:56:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.10_summits.bed INFO @ Wed, 22 Jul 2020 11:56:06: Done! pass1 - making usageList (60 chroms): 1 millis pass2 - checking and writing primary data (1263 records, 4 fields): 518 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 11:56:38: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.20_peaks.xls INFO @ Wed, 22 Jul 2020 11:56:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 11:56:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3919491/SRX3919491.20_summits.bed INFO @ Wed, 22 Jul 2020 11:56:38: Done! pass1 - making usageList (56 chroms): 1 millis pass2 - checking and writing primary data (650 records, 4 fields): 4 millis CompletedMACS2peakCalling