[2023-03-14 12:03:55,348] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:03:55,352] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:03:55,352] [INFO] DQC Reference Directory: /var/lib/cwl/stg47253772-5b42-4fef-9875-0c013e8f19d9/dqc_reference
[2023-03-14 12:03:56,866] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:03:56,866] [INFO] Task started: Prodigal
[2023-03-14 12:03:56,866] [INFO] Running command: cat /var/lib/cwl/stg18dd3670-e2d9-4652-bbf3-7eb0b38b9a44/OceanDNA-b32723.fa | prodigal -d OceanDNA-b32723/cds.fna -a OceanDNA-b32723/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:04:13,052] [INFO] Task succeeded: Prodigal
[2023-03-14 12:04:13,052] [INFO] Task started: HMMsearch
[2023-03-14 12:04:13,052] [INFO] Running command: hmmsearch --tblout OceanDNA-b32723/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47253772-5b42-4fef-9875-0c013e8f19d9/dqc_reference/reference_markers.hmm OceanDNA-b32723/protein.faa > /dev/null
[2023-03-14 12:04:13,279] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:04:13,280] [INFO] Found 6/6 markers.
[2023-03-14 12:04:13,312] [INFO] Query marker FASTA was written to OceanDNA-b32723/markers.fasta
[2023-03-14 12:04:13,312] [INFO] Task started: Blastn
[2023-03-14 12:04:13,312] [INFO] Running command: blastn -query OceanDNA-b32723/markers.fasta -db /var/lib/cwl/stg47253772-5b42-4fef-9875-0c013e8f19d9/dqc_reference/reference_markers.fasta -out OceanDNA-b32723/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:04:14,104] [INFO] Task succeeded: Blastn
[2023-03-14 12:04:14,109] [INFO] Selected 31 target genomes.
[2023-03-14 12:04:14,109] [INFO] Target genome list was writen to OceanDNA-b32723/target_genomes.txt
[2023-03-14 12:04:14,127] [INFO] Task started: fastANI
[2023-03-14 12:04:14,127] [INFO] Running command: fastANI --query /var/lib/cwl/stg18dd3670-e2d9-4652-bbf3-7eb0b38b9a44/OceanDNA-b32723.fa --refList OceanDNA-b32723/target_genomes.txt --output OceanDNA-b32723/fastani_result.tsv --threads 1
[2023-03-14 12:04:38,184] [INFO] Task succeeded: fastANI
[2023-03-14 12:04:38,185] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47253772-5b42-4fef-9875-0c013e8f19d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:04:38,185] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47253772-5b42-4fef-9875-0c013e8f19d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:04:38,201] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:04:38,201] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:04:38,201] [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
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.5956	85	845	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.4706	123	845	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.419	123	845	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.4167	133	845	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.3645	101	845	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.3618	115	845	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.1992	151	845	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	76.198	118	845	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.1597	102	845	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.1523	150	845	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	76.0075	117	845	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	75.9985	118	845	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	75.9902	127	845	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	75.9463	131	845	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	75.9361	116	845	95	below_threshold
Afifella pfennigii	strain=DSM 17143	GCA_000688515.1	209897	209897	type	True	75.9138	67	845	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	75.902	131	845	95	below_threshold
Stappia taiwanensis	strain=DSM 23284	GCA_013868145.1	992267	992267	type	True	75.8737	78	845	95	below_threshold
Stappia taiwanensis	strain=CCM 7757	GCA_014635285.1	992267	992267	type	True	75.8582	79	845	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	75.8529	64	845	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	75.8494	118	845	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	75.8422	70	845	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	75.8335	65	845	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	75.8239	119	845	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	75.804	73	845	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	75.7778	110	845	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	75.5953	82	845	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	75.2819	63	845	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.2426	65	845	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:04:38,202] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32723/tc_result.tsv
[2023-03-14 12:04:38,202] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:04:38,202] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:04:38,202] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47253772-5b42-4fef-9875-0c013e8f19d9/dqc_reference/checkm_data
[2023-03-14 12:04:38,203] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:04:38,227] [INFO] Task started: CheckM
[2023-03-14 12:04:38,227] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32723/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32723/checkm_input OceanDNA-b32723/checkm_result
[2023-03-14 12:05:19,645] [INFO] Task succeeded: CheckM
[2023-03-14 12:05:19,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:05:19,685] [INFO] ===== Completeness check finished =====
[2023-03-14 12:05:19,685] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:05:19,685] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32723/markers.fasta)
[2023-03-14 12:05:19,686] [INFO] Task started: Blastn
[2023-03-14 12:05:19,686] [INFO] Running command: blastn -query OceanDNA-b32723/markers.fasta -db /var/lib/cwl/stg47253772-5b42-4fef-9875-0c013e8f19d9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32723/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:05:21,238] [INFO] Task succeeded: Blastn
[2023-03-14 12:05:21,242] [INFO] Selected 12 target genomes.
[2023-03-14 12:05:21,242] [INFO] Target genome list was writen to OceanDNA-b32723/target_genomes_gtdb.txt
[2023-03-14 12:05:21,253] [INFO] Task started: fastANI
[2023-03-14 12:05:21,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg18dd3670-e2d9-4652-bbf3-7eb0b38b9a44/OceanDNA-b32723.fa --refList OceanDNA-b32723/target_genomes_gtdb.txt --output OceanDNA-b32723/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:05:29,355] [INFO] Task succeeded: fastANI
[2023-03-14 12:05:29,362] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:05:29,363] [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_002727315.1	s__UBA8079 sp002727315	99.9236	661	845	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018667335.1	s__UBA8079 sp018667335	79.3787	534	845	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.89	99.79	0.96	0.96	6	-
GCA_018702955.1	s__UBA8079 sp018702955	79.3074	514	845	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.54	99.39	0.93	0.91	5	-
GCA_002724635.1	s__UBA8079 sp002724635	78.5711	387	845	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643325.1	s__JABJAG01 sp017643325	78.5508	330	845	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722515.1	s__UBA8079 sp002722515	77.2397	161	845	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666195.1	s__JABJAG01 sp018666195	77.0461	220	845	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691025.1	s__SHWB01 sp009691025	76.5901	97	845	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__SHWB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006739055.1	s__Stella vacuolata	76.2162	141	845	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876115.1	s__Azospirillum picis	76.198	118	845	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700095.1	s__Jiella sp002700095	75.8671	70	845	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:05:29,367] [INFO] GTDB search result was written to OceanDNA-b32723/result_gtdb.tsv
[2023-03-14 12:05:29,374] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:05:29,379] [INFO] DFAST_QC result json was written to OceanDNA-b32723/dqc_result.json
[2023-03-14 12:05:29,379] [INFO] DFAST_QC completed!
[2023-03-14 12:05:29,379] [INFO] Total running time: 0h1m34s