[2024-01-25 19:11:35,614] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:11:35,617] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:11:35,617] [INFO] DQC Reference Directory: /var/lib/cwl/stg9877d3db-97d7-4e6d-9bad-b117d8e7cd78/dqc_reference
[2024-01-25 19:11:36,790] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:11:36,791] [INFO] Task started: Prodigal
[2024-01-25 19:11:36,791] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa6fcce7-c4d3-4b01-9386-3d940dced026/GCF_016583645.1_ASM1658364v1_genomic.fna.gz | prodigal -d GCF_016583645.1_ASM1658364v1_genomic.fna/cds.fna -a GCF_016583645.1_ASM1658364v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:11:49,306] [INFO] Task succeeded: Prodigal
[2024-01-25 19:11:49,306] [INFO] Task started: HMMsearch
[2024-01-25 19:11:49,306] [INFO] Running command: hmmsearch --tblout GCF_016583645.1_ASM1658364v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9877d3db-97d7-4e6d-9bad-b117d8e7cd78/dqc_reference/reference_markers.hmm GCF_016583645.1_ASM1658364v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:11:49,620] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:11:49,621] [INFO] Found 6/6 markers.
[2024-01-25 19:11:49,673] [INFO] Query marker FASTA was written to GCF_016583645.1_ASM1658364v1_genomic.fna/markers.fasta
[2024-01-25 19:11:49,674] [INFO] Task started: Blastn
[2024-01-25 19:11:49,674] [INFO] Running command: blastn -query GCF_016583645.1_ASM1658364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9877d3db-97d7-4e6d-9bad-b117d8e7cd78/dqc_reference/reference_markers.fasta -out GCF_016583645.1_ASM1658364v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:50,546] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:50,551] [INFO] Selected 22 target genomes.
[2024-01-25 19:11:50,551] [INFO] Target genome list was writen to GCF_016583645.1_ASM1658364v1_genomic.fna/target_genomes.txt
[2024-01-25 19:11:50,582] [INFO] Task started: fastANI
[2024-01-25 19:11:50,583] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa6fcce7-c4d3-4b01-9386-3d940dced026/GCF_016583645.1_ASM1658364v1_genomic.fna.gz --refList GCF_016583645.1_ASM1658364v1_genomic.fna/target_genomes.txt --output GCF_016583645.1_ASM1658364v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:12:13,058] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:13,058] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9877d3db-97d7-4e6d-9bad-b117d8e7cd78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:12:13,059] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9877d3db-97d7-4e6d-9bad-b117d8e7cd78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:12:13,071] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:12:13,072] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:12:13,072] [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
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	100.0	1749	1762	95	conclusive
Rhodovibrio salinarum	strain=DSM 9154	GCA_000515255.1	1087	1087	type	True	84.9966	933	1762	95	below_threshold
Rhodovibrio salinarum	strain=DSM 9154	GCA_016583505.1	1087	1087	type	True	84.9533	930	1762	95	below_threshold
Ferruginivarius sediminum	strain=WD2A32	GCA_003344765.1	2661937	2661937	type	True	78.8849	483	1762	95	below_threshold
Limimonas halophila	strain=DSM 25584	GCA_900100655.1	1082479	1082479	type	True	78.2945	420	1762	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	77.738	583	1762	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	77.7079	416	1762	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	77.7069	593	1762	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	77.4192	480	1762	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	77.2103	271	1762	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.8053	347	1762	95	below_threshold
Geminicoccus roseus	strain=DSM 18922	GCA_000427665.1	404900	404900	type	True	76.696	303	1762	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.6644	261	1762	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.6446	210	1762	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	76.6346	308	1762	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.5031	353	1762	95	below_threshold
Hansschlegelia beijingensis	strain=DSM 25481	GCA_014196425.1	1133344	1133344	type	True	76.4887	209	1762	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.4737	353	1762	95	below_threshold
Elioraea rosea	strain=PF-30	GCA_007644105.1	2492390	2492390	type	True	76.4071	236	1762	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.3678	368	1762	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.3198	276	1762	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	75.6552	161	1762	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:12:13,073] [INFO] DFAST Taxonomy check result was written to GCF_016583645.1_ASM1658364v1_genomic.fna/tc_result.tsv
[2024-01-25 19:12:13,074] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:12:13,074] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:12:13,074] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9877d3db-97d7-4e6d-9bad-b117d8e7cd78/dqc_reference/checkm_data
[2024-01-25 19:12:13,075] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:12:13,129] [INFO] Task started: CheckM
[2024-01-25 19:12:13,129] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016583645.1_ASM1658364v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016583645.1_ASM1658364v1_genomic.fna/checkm_input GCF_016583645.1_ASM1658364v1_genomic.fna/checkm_result
[2024-01-25 19:12:49,056] [INFO] Task succeeded: CheckM
[2024-01-25 19:12:49,057] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:12:49,093] [INFO] ===== Completeness check finished =====
[2024-01-25 19:12:49,093] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:12:49,094] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016583645.1_ASM1658364v1_genomic.fna/markers.fasta)
[2024-01-25 19:12:49,094] [INFO] Task started: Blastn
[2024-01-25 19:12:49,094] [INFO] Running command: blastn -query GCF_016583645.1_ASM1658364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9877d3db-97d7-4e6d-9bad-b117d8e7cd78/dqc_reference/reference_markers_gtdb.fasta -out GCF_016583645.1_ASM1658364v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:50,751] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:50,755] [INFO] Selected 20 target genomes.
[2024-01-25 19:12:50,755] [INFO] Target genome list was writen to GCF_016583645.1_ASM1658364v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:12:50,784] [INFO] Task started: fastANI
[2024-01-25 19:12:50,784] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa6fcce7-c4d3-4b01-9386-3d940dced026/GCF_016583645.1_ASM1658364v1_genomic.fna.gz --refList GCF_016583645.1_ASM1658364v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016583645.1_ASM1658364v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:13:10,469] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:10,482] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:13:10,482] [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
GCF_016583645.1	s__Rhodovibrio sodomensis	100.0	1749	1762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Rhodovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000515255.1	s__Rhodovibrio salinarum	84.9683	936	1762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Rhodovibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003344765.1	s__Ferruginivarius sediminum	78.8975	481	1762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Ferruginivarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100655.1	s__Limimonas halophila	78.2851	421	1762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Limimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014925385.1	s__WHTV01 sp014925385	77.7153	415	1762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	77.707	594	1762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_007127165.1	s__SKZV01 sp007127165	77.4759	269	1762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__SKZV01	95.0	99.42	99.10	0.91	0.89	3	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	77.4212	478	1762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100455.1	s__Roseospirillum parvum	77.169	276	1762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Roseospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230255.1	s__Caenispirillum bisanense	77.0241	381	1762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423185.1	s__Inquilinus limosus	76.8405	439	1762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869645.1	s__SHVW01 sp016869645	76.7144	274	1762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427665.1	s__Geminicoccus roseus	76.6813	305	1762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__Geminicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016212565.1	s__JACRFY01 sp016212565	76.6279	213	1762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JACRFY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	76.5574	304	1762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006738645.1	s__Stella humosa	76.4917	355	1762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016872535.1	s__2-12-FULL-67-15 sp016872535	76.4496	209	1762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__2-12-FULL-67-15	95.0	95.80	95.80	0.86	0.86	2	-
GCF_007644105.1	s__Elioraea_A rosea	76.3996	237	1762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Elioraea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016214145.1	s__Desulfobacillus sp016214145	75.7929	133	1762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242275.1	s__ZC4RG30 sp003242275	75.6281	108	1762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG30	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:13:10,483] [INFO] GTDB search result was written to GCF_016583645.1_ASM1658364v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:13:10,484] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:13:10,488] [INFO] DFAST_QC result json was written to GCF_016583645.1_ASM1658364v1_genomic.fna/dqc_result.json
[2024-01-25 19:13:10,488] [INFO] DFAST_QC completed!
[2024-01-25 19:13:10,488] [INFO] Total running time: 0h1m35s