[2023-06-28 12:49:49,419] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:49:49,423] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:49:49,423] [INFO] DQC Reference Directory: /var/lib/cwl/stg75c2bcd0-11c0-4bc4-ba5f-6a6c00907c4d/dqc_reference
[2023-06-28 12:49:51,112] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:49:51,112] [INFO] Task started: Prodigal
[2023-06-28 12:49:51,113] [INFO] Running command: gunzip -c /var/lib/cwl/stg84510b91-490e-45de-8328-302f2d27c801/GCA_020852355.1_ASM2085235v1_genomic.fna.gz | prodigal -d GCA_020852355.1_ASM2085235v1_genomic.fna/cds.fna -a GCA_020852355.1_ASM2085235v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:50:04,159] [INFO] Task succeeded: Prodigal
[2023-06-28 12:50:04,159] [INFO] Task started: HMMsearch
[2023-06-28 12:50:04,160] [INFO] Running command: hmmsearch --tblout GCA_020852355.1_ASM2085235v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75c2bcd0-11c0-4bc4-ba5f-6a6c00907c4d/dqc_reference/reference_markers.hmm GCA_020852355.1_ASM2085235v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:50:04,463] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:50:04,465] [INFO] Found 6/6 markers.
[2023-06-28 12:50:04,523] [INFO] Query marker FASTA was written to GCA_020852355.1_ASM2085235v1_genomic.fna/markers.fasta
[2023-06-28 12:50:04,523] [INFO] Task started: Blastn
[2023-06-28 12:50:04,523] [INFO] Running command: blastn -query GCA_020852355.1_ASM2085235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75c2bcd0-11c0-4bc4-ba5f-6a6c00907c4d/dqc_reference/reference_markers.fasta -out GCA_020852355.1_ASM2085235v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:50:05,493] [INFO] Task succeeded: Blastn
[2023-06-28 12:50:05,500] [INFO] Selected 25 target genomes.
[2023-06-28 12:50:05,500] [INFO] Target genome list was writen to GCA_020852355.1_ASM2085235v1_genomic.fna/target_genomes.txt
[2023-06-28 12:50:05,502] [INFO] Task started: fastANI
[2023-06-28 12:50:05,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg84510b91-490e-45de-8328-302f2d27c801/GCA_020852355.1_ASM2085235v1_genomic.fna.gz --refList GCA_020852355.1_ASM2085235v1_genomic.fna/target_genomes.txt --output GCA_020852355.1_ASM2085235v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:50:33,837] [INFO] Task succeeded: fastANI
[2023-06-28 12:50:33,838] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75c2bcd0-11c0-4bc4-ba5f-6a6c00907c4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:50:33,838] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75c2bcd0-11c0-4bc4-ba5f-6a6c00907c4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:50:33,858] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:50:33,858] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:50:33,859] [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
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	82.1809	1045	1625	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	82.1732	1034	1625	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	77.2817	576	1625	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	77.2123	326	1625	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	77.2085	663	1625	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	77.2079	670	1625	95	below_threshold
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	77.1733	487	1625	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	77.1379	565	1625	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	77.1257	363	1625	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	77.1104	485	1625	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.9809	582	1625	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	76.9665	508	1625	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.9576	390	1625	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	76.9501	540	1625	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	76.9308	503	1625	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	76.9244	506	1625	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.888	463	1625	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.8685	414	1625	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.8148	283	1625	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.7398	510	1625	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	76.4688	369	1625	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.1397	377	1625	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	76.106	563	1625	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	76.0942	368	1625	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	75.55	357	1625	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:50:33,860] [INFO] DFAST Taxonomy check result was written to GCA_020852355.1_ASM2085235v1_genomic.fna/tc_result.tsv
[2023-06-28 12:50:33,861] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:50:33,861] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:50:33,861] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75c2bcd0-11c0-4bc4-ba5f-6a6c00907c4d/dqc_reference/checkm_data
[2023-06-28 12:50:33,862] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:50:33,926] [INFO] Task started: CheckM
[2023-06-28 12:50:33,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020852355.1_ASM2085235v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020852355.1_ASM2085235v1_genomic.fna/checkm_input GCA_020852355.1_ASM2085235v1_genomic.fna/checkm_result
[2023-06-28 12:51:33,253] [INFO] Task succeeded: CheckM
[2023-06-28 12:51:33,255] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.69%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:51:33,280] [INFO] ===== Completeness check finished =====
[2023-06-28 12:51:33,280] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:51:33,281] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020852355.1_ASM2085235v1_genomic.fna/markers.fasta)
[2023-06-28 12:51:33,281] [INFO] Task started: Blastn
[2023-06-28 12:51:33,281] [INFO] Running command: blastn -query GCA_020852355.1_ASM2085235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75c2bcd0-11c0-4bc4-ba5f-6a6c00907c4d/dqc_reference/reference_markers_gtdb.fasta -out GCA_020852355.1_ASM2085235v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:51:35,128] [INFO] Task succeeded: Blastn
[2023-06-28 12:51:35,133] [INFO] Selected 17 target genomes.
[2023-06-28 12:51:35,133] [INFO] Target genome list was writen to GCA_020852355.1_ASM2085235v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:51:35,137] [INFO] Task started: fastANI
[2023-06-28 12:51:35,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg84510b91-490e-45de-8328-302f2d27c801/GCA_020852355.1_ASM2085235v1_genomic.fna.gz --refList GCA_020852355.1_ASM2085235v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020852355.1_ASM2085235v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:51:54,795] [INFO] Task succeeded: fastANI
[2023-06-28 12:51:54,814] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 12:51:54,815] [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_006739055.1	s__Stella vacuolata	82.458	1060	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006738645.1	s__Stella humosa	82.1876	1032	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_006738865.1	s__Stella sp006738865	81.8502	1000	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	77.4228	551	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869645.1	s__SHVW01 sp016869645	77.3748	463	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	77.2765	578	1625	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_900177295.1	s__Tistlia consotensis	77.2745	655	1625	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_018401495.1	s__Thalassobaculum_A sp018401495	77.1303	500	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	77.0141	518	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195085.1	s__JACQAG01 sp016195085	77.0113	372	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__JACQAG01	95.0	99.88	99.88	0.96	0.96	2	-
GCF_017356015.1	s__Azospirillum sp017356015	76.9997	448	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876095.1	s__Azospirillum agricola	76.9663	584	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	96.88	96.88	0.87	0.87	2	-
GCF_017876155.1	s__Azospirillum rugosum	76.9646	509	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232485.1	s__JADFZP01 sp015232485	76.8599	260	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	96.70	95.97	0.70	0.69	3	-
GCA_016869145.1	s__VGEU01 sp016869145	76.7747	380	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__VGEU01;g__VGEU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729425.1	s__Phaeospirillum sp902729425	76.6082	300	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197795.1	s__Rhodospira goensis	76.4814	367	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:51:54,817] [INFO] GTDB search result was written to GCA_020852355.1_ASM2085235v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:51:54,817] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:51:54,822] [INFO] DFAST_QC result json was written to GCA_020852355.1_ASM2085235v1_genomic.fna/dqc_result.json
[2023-06-28 12:51:54,822] [INFO] DFAST_QC completed!
[2023-06-28 12:51:54,822] [INFO] Total running time: 0h2m5s