Job ID = 14518000 SRX = SRX10533673 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-01-14T22:03:32 prefetch.2.10.7: 1) Downloading 'SRR14165386'... 2022-01-14T22:03:32 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:03:42 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:03:42 prefetch.2.10.7: 'SRR14165386' is valid 2022-01-14T22:03:42 prefetch.2.10.7: 1) 'SRR14165386' was downloaded successfully 2022-01-14T22:03:42 prefetch.2.10.7: 'SRR14165386' has 0 unresolved dependencies Read 4000000 spots for SRR14165386/SRR14165386.sra Written 4000000 spots for SRR14165386/SRR14165386.sra 2022-01-14T22:04:03 prefetch.2.10.7: 1) Downloading 'SRR14165387'... 2022-01-14T22:04:03 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:04:12 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:04:12 prefetch.2.10.7: 'SRR14165387' is valid 2022-01-14T22:04:12 prefetch.2.10.7: 1) 'SRR14165387' was downloaded successfully 2022-01-14T22:04:12 prefetch.2.10.7: 'SRR14165387' has 0 unresolved dependencies Read 4000000 spots for SRR14165387/SRR14165387.sra Written 4000000 spots for SRR14165387/SRR14165387.sra 2022-01-14T22:04:33 prefetch.2.10.7: 1) Downloading 'SRR14165388'... 2022-01-14T22:04:33 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:04:41 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:04:41 prefetch.2.10.7: 'SRR14165388' is valid 2022-01-14T22:04:41 prefetch.2.10.7: 1) 'SRR14165388' was downloaded successfully 2022-01-14T22:04:41 prefetch.2.10.7: 'SRR14165388' has 0 unresolved dependencies Read 2552587 spots for SRR14165388/SRR14165388.sra Written 2552587 spots for SRR14165388/SRR14165388.sra 2022-01-14T22:05:02 prefetch.2.10.7: 1) Downloading 'SRR14165389'... 2022-01-14T22:05:02 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:05:12 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:05:12 prefetch.2.10.7: 'SRR14165389' is valid 2022-01-14T22:05:12 prefetch.2.10.7: 1) 'SRR14165389' was downloaded successfully 2022-01-14T22:05:12 prefetch.2.10.7: 'SRR14165389' has 0 unresolved dependencies Read 4000000 spots for SRR14165389/SRR14165389.sra Written 4000000 spots for SRR14165389/SRR14165389.sra 2022-01-14T22:05:39 prefetch.2.10.7: 1) Downloading 'SRR14165390'... 2022-01-14T22:05:39 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:05:48 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:05:49 prefetch.2.10.7: 'SRR14165390' is valid 2022-01-14T22:05:49 prefetch.2.10.7: 1) 'SRR14165390' was downloaded successfully 2022-01-14T22:05:49 prefetch.2.10.7: 'SRR14165390' has 0 unresolved dependencies Read 4000000 spots for SRR14165390/SRR14165390.sra Written 4000000 spots for SRR14165390/SRR14165390.sra 2022-01-14T22:06:08 prefetch.2.10.7: 1) Downloading 'SRR14165391'... 2022-01-14T22:06:08 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:06:18 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:06:19 prefetch.2.10.7: 'SRR14165391' is valid 2022-01-14T22:06:19 prefetch.2.10.7: 1) 'SRR14165391' was downloaded successfully 2022-01-14T22:06:19 prefetch.2.10.7: 'SRR14165391' has 0 unresolved dependencies Read 4000000 spots for SRR14165391/SRR14165391.sra Written 4000000 spots for SRR14165391/SRR14165391.sra 2022-01-14T22:06:39 prefetch.2.10.7: 1) Downloading 'SRR14165392'... 2022-01-14T22:06:39 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:06:50 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:06:51 prefetch.2.10.7: 'SRR14165392' is valid 2022-01-14T22:06:51 prefetch.2.10.7: 1) 'SRR14165392' was downloaded successfully 2022-01-14T22:06:51 prefetch.2.10.7: 'SRR14165392' has 0 unresolved dependencies Read 4000000 spots for SRR14165392/SRR14165392.sra Written 4000000 spots for SRR14165392/SRR14165392.sra 2022-01-14T22:07:18 prefetch.2.10.7: 1) Downloading 'SRR14165393'... 2022-01-14T22:07:18 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:07:28 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:07:28 prefetch.2.10.7: 'SRR14165393' is valid 2022-01-14T22:07:28 prefetch.2.10.7: 1) 'SRR14165393' was downloaded successfully 2022-01-14T22:07:28 prefetch.2.10.7: 'SRR14165393' has 0 unresolved dependencies Read 4000000 spots for SRR14165393/SRR14165393.sra Written 4000000 spots for SRR14165393/SRR14165393.sra 2022-01-14T22:07:47 prefetch.2.10.7: 1) Downloading 'SRR14165394'... 2022-01-14T22:07:47 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:07:56 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:07:57 prefetch.2.10.7: 'SRR14165394' is valid 2022-01-14T22:07:57 prefetch.2.10.7: 1) 'SRR14165394' was downloaded successfully 2022-01-14T22:07:57 prefetch.2.10.7: 'SRR14165394' has 0 unresolved dependencies Read 4000000 spots for SRR14165394/SRR14165394.sra Written 4000000 spots for SRR14165394/SRR14165394.sra 2022-01-14T22:08:16 prefetch.2.10.7: 1) Downloading 'SRR14165395'... 2022-01-14T22:08:16 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:08:26 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:08:26 prefetch.2.10.7: 'SRR14165395' is valid 2022-01-14T22:08:26 prefetch.2.10.7: 1) 'SRR14165395' was downloaded successfully 2022-01-14T22:08:26 prefetch.2.10.7: 'SRR14165395' has 0 unresolved dependencies Read 4000000 spots for SRR14165395/SRR14165395.sra Written 4000000 spots for SRR14165395/SRR14165395.sra 2022-01-14T22:08:50 prefetch.2.10.7: 1) Downloading 'SRR14165396'... 2022-01-14T22:08:50 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:09:02 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:09:02 prefetch.2.10.7: 'SRR14165396' is valid 2022-01-14T22:09:02 prefetch.2.10.7: 1) 'SRR14165396' was downloaded successfully 2022-01-14T22:09:02 prefetch.2.10.7: 'SRR14165396' has 0 unresolved dependencies Read 4000000 spots for SRR14165396/SRR14165396.sra Written 4000000 spots for SRR14165396/SRR14165396.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: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:17:16 42552587 reads; of these: 42552587 (100.00%) were unpaired; of these: 29743166 (69.90%) aligned 0 times 9052616 (21.27%) aligned exactly 1 time 3756805 (8.83%) aligned >1 times 30.10% overall alignment rate Time searching: 00:17:22 Overall time: 00:17:22 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 8 files... [bam_rmdupse_core] 5618034 / 12809421 = 0.4386 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 07:31:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.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 @ Sat, 15 Jan 2022 07:31:28: #1 read tag files... INFO @ Sat, 15 Jan 2022 07:31:28: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 07:31:35: 1000000 INFO @ Sat, 15 Jan 2022 07:31:43: 2000000 INFO @ Sat, 15 Jan 2022 07:31:50: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 07:31:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.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 @ Sat, 15 Jan 2022 07:31:57: #1 read tag files... INFO @ Sat, 15 Jan 2022 07:31:57: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 07:31:58: 4000000 INFO @ Sat, 15 Jan 2022 07:32:06: 5000000 INFO @ Sat, 15 Jan 2022 07:32:07: 1000000 INFO @ Sat, 15 Jan 2022 07:32:14: 6000000 INFO @ Sat, 15 Jan 2022 07:32:18: 2000000 INFO @ Sat, 15 Jan 2022 07:32:22: 7000000 INFO @ Sat, 15 Jan 2022 07:32:23: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 07:32:23: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 07:32:23: #1 total tags in treatment: 7191387 INFO @ Sat, 15 Jan 2022 07:32:23: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 07:32:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 07:32:24: #1 tags after filtering in treatment: 7191149 INFO @ Sat, 15 Jan 2022 07:32:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 07:32:24: #1 finished! INFO @ Sat, 15 Jan 2022 07:32:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 07:32:24: #2 looking for paired plus/minus strand peaks... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 07:32:25: #2 number of paired peaks: 18160 INFO @ Sat, 15 Jan 2022 07:32:25: start model_add_line... INFO @ Sat, 15 Jan 2022 07:32:25: start X-correlation... INFO @ Sat, 15 Jan 2022 07:32:25: end of X-cor INFO @ Sat, 15 Jan 2022 07:32:25: #2 finished! INFO @ Sat, 15 Jan 2022 07:32:25: #2 predicted fragment length is 269 bps INFO @ Sat, 15 Jan 2022 07:32:25: #2 alternative fragment length(s) may be 55,242,269 bps INFO @ Sat, 15 Jan 2022 07:32:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.05_model.r INFO @ Sat, 15 Jan 2022 07:32:25: #3 Call peaks... INFO @ Sat, 15 Jan 2022 07:32:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 07:32:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.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 @ Sat, 15 Jan 2022 07:32:27: #1 read tag files... INFO @ Sat, 15 Jan 2022 07:32:27: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 07:32:28: 3000000 INFO @ Sat, 15 Jan 2022 07:32:35: 1000000 INFO @ Sat, 15 Jan 2022 07:32:39: 4000000 INFO @ Sat, 15 Jan 2022 07:32:42: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 07:32:43: 2000000 INFO @ Sat, 15 Jan 2022 07:32:49: 5000000 INFO @ Sat, 15 Jan 2022 07:32:51: 3000000 INFO @ Sat, 15 Jan 2022 07:32:52: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.05_peaks.xls INFO @ Sat, 15 Jan 2022 07:32:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 07:32:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.05_summits.bed INFO @ Sat, 15 Jan 2022 07:32:52: Done! pass1 - making usageList (76 chroms): 1 millis pass2 - checking and writing primary data (2117 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 07:32:59: 4000000 INFO @ Sat, 15 Jan 2022 07:32:59: 6000000 INFO @ Sat, 15 Jan 2022 07:33:07: 5000000 INFO @ Sat, 15 Jan 2022 07:33:09: 7000000 INFO @ Sat, 15 Jan 2022 07:33:11: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 07:33:11: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 07:33:11: #1 total tags in treatment: 7191387 INFO @ Sat, 15 Jan 2022 07:33:11: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 07:33:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 07:33:11: #1 tags after filtering in treatment: 7191149 INFO @ Sat, 15 Jan 2022 07:33:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 07:33:11: #1 finished! INFO @ Sat, 15 Jan 2022 07:33:11: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 07:33:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 07:33:13: #2 number of paired peaks: 18160 INFO @ Sat, 15 Jan 2022 07:33:13: start model_add_line... INFO @ Sat, 15 Jan 2022 07:33:13: start X-correlation... INFO @ Sat, 15 Jan 2022 07:33:13: end of X-cor INFO @ Sat, 15 Jan 2022 07:33:13: #2 finished! INFO @ Sat, 15 Jan 2022 07:33:13: #2 predicted fragment length is 269 bps INFO @ Sat, 15 Jan 2022 07:33:13: #2 alternative fragment length(s) may be 55,242,269 bps INFO @ Sat, 15 Jan 2022 07:33:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.10_model.r INFO @ Sat, 15 Jan 2022 07:33:13: #3 Call peaks... INFO @ Sat, 15 Jan 2022 07:33:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 07:33:14: 6000000 INFO @ Sat, 15 Jan 2022 07:33:22: 7000000 INFO @ Sat, 15 Jan 2022 07:33:24: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 07:33:24: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 07:33:24: #1 total tags in treatment: 7191387 INFO @ Sat, 15 Jan 2022 07:33:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 07:33:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 07:33:24: #1 tags after filtering in treatment: 7191149 INFO @ Sat, 15 Jan 2022 07:33:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 07:33:24: #1 finished! INFO @ Sat, 15 Jan 2022 07:33:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 07:33:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 07:33:26: #2 number of paired peaks: 18160 INFO @ Sat, 15 Jan 2022 07:33:26: start model_add_line... INFO @ Sat, 15 Jan 2022 07:33:26: start X-correlation... INFO @ Sat, 15 Jan 2022 07:33:26: end of X-cor INFO @ Sat, 15 Jan 2022 07:33:26: #2 finished! INFO @ Sat, 15 Jan 2022 07:33:26: #2 predicted fragment length is 269 bps INFO @ Sat, 15 Jan 2022 07:33:26: #2 alternative fragment length(s) may be 55,242,269 bps INFO @ Sat, 15 Jan 2022 07:33:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.20_model.r INFO @ Sat, 15 Jan 2022 07:33:26: #3 Call peaks... INFO @ Sat, 15 Jan 2022 07:33:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 07:33:30: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 07:33:39: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.10_peaks.xls INFO @ Sat, 15 Jan 2022 07:33:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 07:33:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.10_summits.bed INFO @ Sat, 15 Jan 2022 07:33:39: Done! pass1 - making usageList (61 chroms): 1 millis pass2 - checking and writing primary data (1080 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 07:33:42: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 07:33:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.20_peaks.xls INFO @ Sat, 15 Jan 2022 07:33:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 07:33:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533673/SRX10533673.20_summits.bed INFO @ Sat, 15 Jan 2022 07:33:51: Done! pass1 - making usageList (50 chroms): 0 millis pass2 - checking and writing primary data (467 records, 4 fields): 16 millis CompletedMACS2peakCalling