Job ID = 5721092 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T19:39:00 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 ) 2020-04-15T19:39:00 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 ) 2020-04-15T19:39:00 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 ) 2020-04-15T19:41:22 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 ) 2020-04-15T19:41:22 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 : 34,208,103 reads read : 68,416,206 reads written : 34,208,103 reads 0-length : 34,208,103 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:05 34208103 reads; of these: 34208103 (100.00%) were unpaired; of these: 5018744 (14.67%) aligned 0 times 20342789 (59.47%) aligned exactly 1 time 8846570 (25.86%) aligned >1 times 85.33% overall alignment rate Time searching: 00:14:06 Overall time: 00:14:06 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 12 files... [bam_rmdupse_core] 7675819 / 29189359 = 0.2630 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 05:06:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.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 05:06:58: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:06:58: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:07:04: 1000000 INFO @ Thu, 16 Apr 2020 05:07:10: 2000000 INFO @ Thu, 16 Apr 2020 05:07:15: 3000000 INFO @ Thu, 16 Apr 2020 05:07:21: 4000000 INFO @ Thu, 16 Apr 2020 05:07:26: 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 @ Thu, 16 Apr 2020 05:07:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.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 05:07:28: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:07:28: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:07:32: 6000000 INFO @ Thu, 16 Apr 2020 05:07:34: 1000000 INFO @ Thu, 16 Apr 2020 05:07:37: 7000000 INFO @ Thu, 16 Apr 2020 05:07:40: 2000000 INFO @ Thu, 16 Apr 2020 05:07:43: 8000000 INFO @ Thu, 16 Apr 2020 05:07:45: 3000000 INFO @ Thu, 16 Apr 2020 05:07:48: 9000000 INFO @ Thu, 16 Apr 2020 05:07:51: 4000000 INFO @ Thu, 16 Apr 2020 05:07:54: 10000000 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 05:07:57: 5000000 INFO @ Thu, 16 Apr 2020 05:07:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.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 05:07:58: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:07:58: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:08:00: 11000000 INFO @ Thu, 16 Apr 2020 05:08:03: 6000000 INFO @ Thu, 16 Apr 2020 05:08:04: 1000000 INFO @ Thu, 16 Apr 2020 05:08:05: 12000000 INFO @ Thu, 16 Apr 2020 05:08:08: 7000000 INFO @ Thu, 16 Apr 2020 05:08:10: 2000000 INFO @ Thu, 16 Apr 2020 05:08:11: 13000000 INFO @ Thu, 16 Apr 2020 05:08:14: 8000000 INFO @ Thu, 16 Apr 2020 05:08:15: 3000000 INFO @ Thu, 16 Apr 2020 05:08:17: 14000000 INFO @ Thu, 16 Apr 2020 05:08:20: 9000000 INFO @ Thu, 16 Apr 2020 05:08:21: 4000000 INFO @ Thu, 16 Apr 2020 05:08:23: 15000000 INFO @ Thu, 16 Apr 2020 05:08:26: 10000000 INFO @ Thu, 16 Apr 2020 05:08:27: 5000000 INFO @ Thu, 16 Apr 2020 05:08:28: 16000000 INFO @ Thu, 16 Apr 2020 05:08:31: 11000000 INFO @ Thu, 16 Apr 2020 05:08:32: 6000000 INFO @ Thu, 16 Apr 2020 05:08:34: 17000000 INFO @ Thu, 16 Apr 2020 05:08:37: 12000000 INFO @ Thu, 16 Apr 2020 05:08:38: 7000000 INFO @ Thu, 16 Apr 2020 05:08:40: 18000000 INFO @ Thu, 16 Apr 2020 05:08:43: 13000000 INFO @ Thu, 16 Apr 2020 05:08:43: 8000000 INFO @ Thu, 16 Apr 2020 05:08:45: 19000000 INFO @ Thu, 16 Apr 2020 05:08:49: 14000000 INFO @ Thu, 16 Apr 2020 05:08:49: 9000000 INFO @ Thu, 16 Apr 2020 05:08:51: 20000000 INFO @ Thu, 16 Apr 2020 05:08:54: 15000000 INFO @ Thu, 16 Apr 2020 05:08:55: 10000000 INFO @ Thu, 16 Apr 2020 05:08:57: 21000000 INFO @ Thu, 16 Apr 2020 05:09:00: #1 tag size is determined as 73 bps INFO @ Thu, 16 Apr 2020 05:09:00: #1 tag size = 73 INFO @ Thu, 16 Apr 2020 05:09:00: #1 total tags in treatment: 21513540 INFO @ Thu, 16 Apr 2020 05:09:00: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:09:00: #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 05:09:00: #1 tags after filtering in treatment: 21513540 INFO @ Thu, 16 Apr 2020 05:09:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:09:00: #1 finished! INFO @ Thu, 16 Apr 2020 05:09:00: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:09:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:09:00: 11000000 INFO @ Thu, 16 Apr 2020 05:09:00: 16000000 INFO @ Thu, 16 Apr 2020 05:09:02: #2 number of paired peaks: 1015 INFO @ Thu, 16 Apr 2020 05:09:02: start model_add_line... INFO @ Thu, 16 Apr 2020 05:09:02: start X-correlation... INFO @ Thu, 16 Apr 2020 05:09:02: end of X-cor INFO @ Thu, 16 Apr 2020 05:09:02: #2 finished! INFO @ Thu, 16 Apr 2020 05:09:02: #2 predicted fragment length is 141 bps INFO @ Thu, 16 Apr 2020 05:09:02: #2 alternative fragment length(s) may be 141 bps INFO @ Thu, 16 Apr 2020 05:09:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.05_model.r WARNING @ Thu, 16 Apr 2020 05:09:02: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:09:02: #2 You may need to consider one of the other alternative d(s): 141 WARNING @ Thu, 16 Apr 2020 05:09:02: #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 05:09:02: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:09:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:09:06: 12000000 INFO @ Thu, 16 Apr 2020 05:09:06: 17000000 INFO @ Thu, 16 Apr 2020 05:09:11: 13000000 INFO @ Thu, 16 Apr 2020 05:09:12: 18000000 INFO @ Thu, 16 Apr 2020 05:09:17: 14000000 INFO @ Thu, 16 Apr 2020 05:09:17: 19000000 INFO @ Thu, 16 Apr 2020 05:09:23: 15000000 INFO @ Thu, 16 Apr 2020 05:09:23: 20000000 INFO @ Thu, 16 Apr 2020 05:09:28: 16000000 INFO @ Thu, 16 Apr 2020 05:09:29: 21000000 INFO @ Thu, 16 Apr 2020 05:09:32: #1 tag size is determined as 73 bps INFO @ Thu, 16 Apr 2020 05:09:32: #1 tag size = 73 INFO @ Thu, 16 Apr 2020 05:09:32: #1 total tags in treatment: 21513540 INFO @ Thu, 16 Apr 2020 05:09:32: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:09:32: #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 05:09:32: #1 tags after filtering in treatment: 21513540 INFO @ Thu, 16 Apr 2020 05:09:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:09:32: #1 finished! INFO @ Thu, 16 Apr 2020 05:09:32: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:09:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:09:34: #2 number of paired peaks: 1015 INFO @ Thu, 16 Apr 2020 05:09:34: start model_add_line... INFO @ Thu, 16 Apr 2020 05:09:34: start X-correlation... INFO @ Thu, 16 Apr 2020 05:09:34: end of X-cor INFO @ Thu, 16 Apr 2020 05:09:34: #2 finished! INFO @ Thu, 16 Apr 2020 05:09:34: #2 predicted fragment length is 141 bps INFO @ Thu, 16 Apr 2020 05:09:34: #2 alternative fragment length(s) may be 141 bps INFO @ Thu, 16 Apr 2020 05:09:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.10_model.r WARNING @ Thu, 16 Apr 2020 05:09:34: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:09:34: #2 You may need to consider one of the other alternative d(s): 141 WARNING @ Thu, 16 Apr 2020 05:09:34: #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 05:09:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:09:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:09:34: 17000000 INFO @ Thu, 16 Apr 2020 05:09:39: 18000000 INFO @ Thu, 16 Apr 2020 05:09:45: 19000000 INFO @ Thu, 16 Apr 2020 05:09:48: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:09:50: 20000000 INFO @ Thu, 16 Apr 2020 05:09:56: 21000000 INFO @ Thu, 16 Apr 2020 05:09:59: #1 tag size is determined as 73 bps INFO @ Thu, 16 Apr 2020 05:09:59: #1 tag size = 73 INFO @ Thu, 16 Apr 2020 05:09:59: #1 total tags in treatment: 21513540 INFO @ Thu, 16 Apr 2020 05:09:59: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:09:59: #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 05:09:59: #1 tags after filtering in treatment: 21513540 INFO @ Thu, 16 Apr 2020 05:09:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:09:59: #1 finished! INFO @ Thu, 16 Apr 2020 05:09:59: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:09:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:10:01: #2 number of paired peaks: 1015 INFO @ Thu, 16 Apr 2020 05:10:01: start model_add_line... INFO @ Thu, 16 Apr 2020 05:10:01: start X-correlation... INFO @ Thu, 16 Apr 2020 05:10:01: end of X-cor INFO @ Thu, 16 Apr 2020 05:10:01: #2 finished! INFO @ Thu, 16 Apr 2020 05:10:01: #2 predicted fragment length is 141 bps INFO @ Thu, 16 Apr 2020 05:10:01: #2 alternative fragment length(s) may be 141 bps INFO @ Thu, 16 Apr 2020 05:10:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.20_model.r WARNING @ Thu, 16 Apr 2020 05:10:01: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:10:01: #2 You may need to consider one of the other alternative d(s): 141 WARNING @ Thu, 16 Apr 2020 05:10:01: #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 05:10:01: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:10:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:10:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:10:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:10:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.05_summits.bed INFO @ Thu, 16 Apr 2020 05:10:10: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8765 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:10:20: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:10:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:10:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:10:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.10_summits.bed INFO @ Thu, 16 Apr 2020 05:10:42: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6967 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:10:46: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:11:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:11:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:11:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6685747/SRX6685747.20_summits.bed INFO @ Thu, 16 Apr 2020 05:11:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5208 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。