[2023-03-18 23:22:48,498] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:22:48,498] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:22:48,498] [INFO] DQC Reference Directory: /var/lib/cwl/stg318960b0-fd07-47dc-8225-0900a7d19cd9/dqc_reference
[2023-03-18 23:22:49,618] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:22:49,618] [INFO] Task started: Prodigal
[2023-03-18 23:22:49,619] [INFO] Running command: cat /var/lib/cwl/stga6e1881c-2fed-4d56-ae1f-77100a701c48/OceanDNA-b22252.fa | prodigal -d OceanDNA-b22252/cds.fna -a OceanDNA-b22252/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:23:09,886] [INFO] Task succeeded: Prodigal
[2023-03-18 23:23:09,886] [INFO] Task started: HMMsearch
[2023-03-18 23:23:09,886] [INFO] Running command: hmmsearch --tblout OceanDNA-b22252/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg318960b0-fd07-47dc-8225-0900a7d19cd9/dqc_reference/reference_markers.hmm OceanDNA-b22252/protein.faa > /dev/null
[2023-03-18 23:23:10,074] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:23:10,075] [INFO] Found 6/6 markers.
[2023-03-18 23:23:10,097] [INFO] Query marker FASTA was written to OceanDNA-b22252/markers.fasta
[2023-03-18 23:23:10,098] [INFO] Task started: Blastn
[2023-03-18 23:23:10,098] [INFO] Running command: blastn -query OceanDNA-b22252/markers.fasta -db /var/lib/cwl/stg318960b0-fd07-47dc-8225-0900a7d19cd9/dqc_reference/reference_markers.fasta -out OceanDNA-b22252/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:23:10,722] [INFO] Task succeeded: Blastn
[2023-03-18 23:23:10,723] [INFO] Selected 27 target genomes.
[2023-03-18 23:23:10,724] [INFO] Target genome list was writen to OceanDNA-b22252/target_genomes.txt
[2023-03-18 23:23:10,740] [INFO] Task started: fastANI
[2023-03-18 23:23:10,740] [INFO] Running command: fastANI --query /var/lib/cwl/stga6e1881c-2fed-4d56-ae1f-77100a701c48/OceanDNA-b22252.fa --refList OceanDNA-b22252/target_genomes.txt --output OceanDNA-b22252/fastani_result.tsv --threads 1
[2023-03-18 23:23:31,440] [INFO] Task succeeded: fastANI
[2023-03-18 23:23:31,440] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg318960b0-fd07-47dc-8225-0900a7d19cd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:23:31,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg318960b0-fd07-47dc-8225-0900a7d19cd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:23:31,453] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:23:31,453] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:23:31,453] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Algisphaera agarilytica	strain=DSM 103725	GCA_014207595.1	1385975	1385975	type	True	76.2565	86	1090	95	below_threshold
Mucisphaera calidilacus	strain=Pan265	GCA_007748075.1	2527982	2527982	type	True	76.2192	75	1090	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	75.6529	153	1090	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	75.6393	154	1090	95	below_threshold
Humisphaera borealis	strain=M1803	GCA_015169395.1	2807512	2807512	type	True	75.477	74	1090	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	75.0637	158	1090	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.8889	132	1090	95	below_threshold
Nakamurella multipartita	strain=DSM 44233	GCA_000024365.1	53461	53461	type	True	74.8057	101	1090	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	74.8015	76	1090	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	74.7908	122	1090	95	below_threshold
Streptomyces cirratus	strain=JCM 4738	GCA_014650775.1	68187	68187	type	True	74.7797	121	1090	95	below_threshold
Roseomonas aerilata	strain=DSM 19363	GCA_000711725.1	452982	452982	type	True	74.7684	75	1090	95	below_threshold
Geodermatophilus pulveris	strain=DSM 46839	GCA_900188375.1	1564159	1564159	type	True	74.7666	116	1090	95	below_threshold
Nonomuraea pusilla	strain=DSM 43357	GCA_900109355.1	46177	46177	type	True	74.7368	163	1090	95	below_threshold
Glycomyces arizonensis	strain=DSM 44726	GCA_000482705.1	256035	256035	type	True	74.7281	87	1090	95	below_threshold
Streptomyces brasiliscabiei	strain=IBSBF 2867	GCA_018927715.1	2736302	2736302	type	True	74.7255	125	1090	95	below_threshold
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	74.7153	159	1090	95	below_threshold
Labedella endophytica	strain=EGI 6500705	GCA_003990045.1	1523160	1523160	type	True	74.6955	56	1090	95	below_threshold
Halorussus halobius	strain=HD8-83	GCA_004765805.1	1710537	1710537	type	True	74.6667	54	1090	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	74.6662	51	1090	95	below_threshold
Agromyces lapidis	strain=JCM 14321	GCA_009749405.1	279574	279574	type	True	74.6283	64	1090	95	below_threshold
Gryllotalpicola protaetiae	strain=2DFW10M-5	GCA_003627055.1	2419771	2419771	type	True	74.5152	54	1090	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:23:31,453] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22252/tc_result.tsv
[2023-03-18 23:23:31,454] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:23:31,454] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:23:31,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg318960b0-fd07-47dc-8225-0900a7d19cd9/dqc_reference/checkm_data
[2023-03-18 23:23:31,454] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:23:31,460] [INFO] Task started: CheckM
[2023-03-18 23:23:31,460] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22252/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22252/checkm_input OceanDNA-b22252/checkm_result
[2023-03-18 23:24:25,376] [INFO] Task succeeded: CheckM
[2023-03-18 23:24:25,376] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:24:25,380] [INFO] ===== Completeness check finished =====
[2023-03-18 23:24:25,380] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:24:25,380] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22252/markers.fasta)
[2023-03-18 23:24:25,381] [INFO] Task started: Blastn
[2023-03-18 23:24:25,381] [INFO] Running command: blastn -query OceanDNA-b22252/markers.fasta -db /var/lib/cwl/stg318960b0-fd07-47dc-8225-0900a7d19cd9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22252/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:24:26,416] [INFO] Task succeeded: Blastn
[2023-03-18 23:24:26,417] [INFO] Selected 19 target genomes.
[2023-03-18 23:24:26,417] [INFO] Target genome list was writen to OceanDNA-b22252/target_genomes_gtdb.txt
[2023-03-18 23:24:26,436] [INFO] Task started: fastANI
[2023-03-18 23:24:26,436] [INFO] Running command: fastANI --query /var/lib/cwl/stga6e1881c-2fed-4d56-ae1f-77100a701c48/OceanDNA-b22252.fa --refList OceanDNA-b22252/target_genomes_gtdb.txt --output OceanDNA-b22252/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:24:36,721] [INFO] Task succeeded: fastANI
[2023-03-18 23:24:36,731] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:24:36,732] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_003696675.1	s__UBA6054 sp003696675	80.433	492	1090	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002429045.1	s__UBA6054 sp002429045	79.074	464	1090	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013285505.1	s__PNC22 sp013285505	78.1069	275	1090	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__PNC22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364005.1	s__UBA1924 sp002364005	77.7504	286	1090	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	99.92	99.89	0.95	0.91	4	-
GCA_017642965.1	s__UBA1924 sp017642965	77.6948	275	1090	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007694925.1	s__SLFH01 sp007694925	77.5532	207	1090	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__SLFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693785.1	s__RECY01 sp007693785	77.4691	220	1090	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007124345.1	s__SLFH01 sp007124345	77.3648	175	1090	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__SLFH01	95.0	98.92	98.92	0.84	0.84	2	-
GCA_002337545.1	s__UBA1924 sp002337545	77.2606	169	1090	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	98.57	98.49	0.90	0.89	3	-
GCA_013360695.1	s__JABWBC01 sp013360695	77.1538	171	1090	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JABWBC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480345.1	s__UBA1926 sp002480345	77.145	212	1090	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1926	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242645.1	s__JAFEBO01 sp018242645	77.0107	125	1090	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JAFEBO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693965.1	s__RECQ01 sp007693965	76.8186	149	1090	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793195.1	s__JABWBC01 sp016793195	76.8098	159	1090	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JABWBC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303565.1	s__JAFLCM01 sp017303565	76.7343	123	1090	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JAFLCM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009827215.1	s__UBA1924 sp009827215	76.0634	69	1090	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764895.1	s__UBA1924 sp016764895	75.7466	55	1090	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113185.1	s__Agromyces sp900113185	74.6899	56	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:24:36,732] [INFO] GTDB search result was written to OceanDNA-b22252/result_gtdb.tsv
[2023-03-18 23:24:36,733] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:24:36,736] [INFO] DFAST_QC result json was written to OceanDNA-b22252/dqc_result.json
[2023-03-18 23:24:36,736] [INFO] DFAST_QC completed!
[2023-03-18 23:24:36,736] [INFO] Total running time: 0h1m48s