Job ID = 5721082 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T19:24:47 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 15,015,506 reads read : 30,031,012 reads written : 30,031,012 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:59:42 15015506 reads; of these: 15015506 (100.00%) were paired; of these: 3883947 (25.87%) aligned concordantly 0 times 2310802 (15.39%) aligned concordantly exactly 1 time 8820757 (58.74%) aligned concordantly >1 times ---- 3883947 pairs aligned concordantly 0 times; of these: 475070 (12.23%) aligned discordantly 1 time ---- 3408877 pairs aligned 0 times concordantly or discordantly; of these: 6817754 mates make up the pairs; of these: 2977876 (43.68%) aligned 0 times 1146594 (16.82%) aligned exactly 1 time 2693284 (39.50%) aligned >1 times 90.08% overall alignment rate Time searching: 01:59:42 Overall time: 01:59:42 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 4264647 / 11203596 = 0.3806 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 @ Thu, 16 Apr 2020 06:52:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 06:52:49: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:52:49: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:52:57: 1000000 INFO @ Thu, 16 Apr 2020 06:53:06: 2000000 INFO @ Thu, 16 Apr 2020 06:53:14: 3000000 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 @ Thu, 16 Apr 2020 06:53:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 06:53:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:53:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:53:23: 4000000 INFO @ Thu, 16 Apr 2020 06:53:28: 1000000 INFO @ Thu, 16 Apr 2020 06:53:33: 5000000 INFO @ Thu, 16 Apr 2020 06:53:38: 2000000 INFO @ Thu, 16 Apr 2020 06:53:43: 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 @ Thu, 16 Apr 2020 06:53:48: 3000000 INFO @ Thu, 16 Apr 2020 06:53:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 06:53:48: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:53:48: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:53:53: 7000000 INFO @ Thu, 16 Apr 2020 06:53:58: 4000000 INFO @ Thu, 16 Apr 2020 06:53:59: 1000000 INFO @ Thu, 16 Apr 2020 06:54:03: 8000000 INFO @ Thu, 16 Apr 2020 06:54:08: 5000000 INFO @ Thu, 16 Apr 2020 06:54:09: 2000000 INFO @ Thu, 16 Apr 2020 06:54:13: 9000000 INFO @ Thu, 16 Apr 2020 06:54:18: 6000000 INFO @ Thu, 16 Apr 2020 06:54:19: 3000000 INFO @ Thu, 16 Apr 2020 06:54:23: 10000000 INFO @ Thu, 16 Apr 2020 06:54:28: 7000000 INFO @ Thu, 16 Apr 2020 06:54:29: 4000000 INFO @ Thu, 16 Apr 2020 06:54:33: 11000000 INFO @ Thu, 16 Apr 2020 06:54:38: 8000000 INFO @ Thu, 16 Apr 2020 06:54:39: 5000000 INFO @ Thu, 16 Apr 2020 06:54:43: 12000000 INFO @ Thu, 16 Apr 2020 06:54:48: 9000000 INFO @ Thu, 16 Apr 2020 06:54:49: 6000000 INFO @ Thu, 16 Apr 2020 06:54:53: 13000000 INFO @ Thu, 16 Apr 2020 06:54:58: 10000000 INFO @ Thu, 16 Apr 2020 06:54:59: 7000000 INFO @ Thu, 16 Apr 2020 06:55:02: 14000000 INFO @ Thu, 16 Apr 2020 06:55:08: 11000000 INFO @ Thu, 16 Apr 2020 06:55:09: 8000000 INFO @ Thu, 16 Apr 2020 06:55:12: 15000000 INFO @ Thu, 16 Apr 2020 06:55:17: 12000000 INFO @ Thu, 16 Apr 2020 06:55:19: 9000000 INFO @ Thu, 16 Apr 2020 06:55:22: 16000000 INFO @ Thu, 16 Apr 2020 06:55:27: 13000000 INFO @ Thu, 16 Apr 2020 06:55:29: 10000000 INFO @ Thu, 16 Apr 2020 06:55:33: 17000000 INFO @ Thu, 16 Apr 2020 06:55:37: 14000000 INFO @ Thu, 16 Apr 2020 06:55:39: 11000000 INFO @ Thu, 16 Apr 2020 06:55:43: 18000000 INFO @ Thu, 16 Apr 2020 06:55:47: 15000000 INFO @ Thu, 16 Apr 2020 06:55:48: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 06:55:48: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 06:55:48: #1 total tags in treatment: 6912644 INFO @ Thu, 16 Apr 2020 06:55:48: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:55:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:55:48: #1 tags after filtering in treatment: 5338415 INFO @ Thu, 16 Apr 2020 06:55:48: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 16 Apr 2020 06:55:48: #1 finished! INFO @ Thu, 16 Apr 2020 06:55:48: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:55:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:55:48: #2 number of paired peaks: 6601 INFO @ Thu, 16 Apr 2020 06:55:48: start model_add_line... INFO @ Thu, 16 Apr 2020 06:55:48: start X-correlation... INFO @ Thu, 16 Apr 2020 06:55:49: end of X-cor INFO @ Thu, 16 Apr 2020 06:55:49: #2 finished! INFO @ Thu, 16 Apr 2020 06:55:49: #2 predicted fragment length is 202 bps INFO @ Thu, 16 Apr 2020 06:55:49: #2 alternative fragment length(s) may be 202 bps INFO @ Thu, 16 Apr 2020 06:55:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.05_model.r WARNING @ Thu, 16 Apr 2020 06:55:49: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:55:49: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Thu, 16 Apr 2020 06:55:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:55:49: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:55:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:55:49: 12000000 INFO @ Thu, 16 Apr 2020 06:55:57: 16000000 INFO @ Thu, 16 Apr 2020 06:55:58: 13000000 INFO @ Thu, 16 Apr 2020 06:56:03: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:56:07: 17000000 INFO @ Thu, 16 Apr 2020 06:56:08: 14000000 INFO @ Thu, 16 Apr 2020 06:56:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:56:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:56:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.05_summits.bed INFO @ Thu, 16 Apr 2020 06:56:10: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (13496 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:56:17: 18000000 INFO @ Thu, 16 Apr 2020 06:56:17: 15000000 INFO @ Thu, 16 Apr 2020 06:56:21: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 06:56:21: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 06:56:21: #1 total tags in treatment: 6912644 INFO @ Thu, 16 Apr 2020 06:56:21: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:56:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:56:22: #1 tags after filtering in treatment: 5338415 INFO @ Thu, 16 Apr 2020 06:56:22: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 16 Apr 2020 06:56:22: #1 finished! INFO @ Thu, 16 Apr 2020 06:56:22: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:56:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:56:22: #2 number of paired peaks: 6601 INFO @ Thu, 16 Apr 2020 06:56:22: start model_add_line... INFO @ Thu, 16 Apr 2020 06:56:22: start X-correlation... INFO @ Thu, 16 Apr 2020 06:56:22: end of X-cor INFO @ Thu, 16 Apr 2020 06:56:22: #2 finished! INFO @ Thu, 16 Apr 2020 06:56:22: #2 predicted fragment length is 202 bps INFO @ Thu, 16 Apr 2020 06:56:22: #2 alternative fragment length(s) may be 202 bps INFO @ Thu, 16 Apr 2020 06:56:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.10_model.r WARNING @ Thu, 16 Apr 2020 06:56:22: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:56:22: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Thu, 16 Apr 2020 06:56:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:56:22: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:56:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:56:27: 16000000 INFO @ Thu, 16 Apr 2020 06:56:36: 17000000 INFO @ Thu, 16 Apr 2020 06:56:37: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:56:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:56:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:56:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.10_summits.bed INFO @ Thu, 16 Apr 2020 06:56:44: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (9079 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:56:45: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 06:56:50: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 06:56:50: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 06:56:50: #1 total tags in treatment: 6912644 INFO @ Thu, 16 Apr 2020 06:56:50: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:56:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:56:50: #1 tags after filtering in treatment: 5338415 INFO @ Thu, 16 Apr 2020 06:56:50: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 16 Apr 2020 06:56:50: #1 finished! INFO @ Thu, 16 Apr 2020 06:56:50: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:56:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:56:51: #2 number of paired peaks: 6601 INFO @ Thu, 16 Apr 2020 06:56:51: start model_add_line... INFO @ Thu, 16 Apr 2020 06:56:51: start X-correlation... INFO @ Thu, 16 Apr 2020 06:56:51: end of X-cor INFO @ Thu, 16 Apr 2020 06:56:51: #2 finished! INFO @ Thu, 16 Apr 2020 06:56:51: #2 predicted fragment length is 202 bps INFO @ Thu, 16 Apr 2020 06:56:51: #2 alternative fragment length(s) may be 202 bps INFO @ Thu, 16 Apr 2020 06:56:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.20_model.r WARNING @ Thu, 16 Apr 2020 06:56:51: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:56:51: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Thu, 16 Apr 2020 06:56:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:56:51: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:56:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:57:06: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:57:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:57:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:57:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448076/SRX6448076.20_summits.bed INFO @ Thu, 16 Apr 2020 06:57:12: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4532 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。