[2024-01-24 13:27:46,372] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:46,374] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:46,374] [INFO] DQC Reference Directory: /var/lib/cwl/stg59a5e874-4b3b-46db-88e6-31e742032bb2/dqc_reference
[2024-01-24 13:27:47,845] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:47,847] [INFO] Task started: Prodigal
[2024-01-24 13:27:47,848] [INFO] Running command: gunzip -c /var/lib/cwl/stgfca1887a-d5a0-405b-8522-4a067562a780/GCF_019966545.1_ASM1996654v1_genomic.fna.gz | prodigal -d GCF_019966545.1_ASM1996654v1_genomic.fna/cds.fna -a GCF_019966545.1_ASM1996654v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:04,838] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:04,838] [INFO] Task started: HMMsearch
[2024-01-24 13:28:04,838] [INFO] Running command: hmmsearch --tblout GCF_019966545.1_ASM1996654v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59a5e874-4b3b-46db-88e6-31e742032bb2/dqc_reference/reference_markers.hmm GCF_019966545.1_ASM1996654v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:05,247] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:05,250] [INFO] Found 6/6 markers.
[2024-01-24 13:28:05,304] [INFO] Query marker FASTA was written to GCF_019966545.1_ASM1996654v1_genomic.fna/markers.fasta
[2024-01-24 13:28:05,304] [INFO] Task started: Blastn
[2024-01-24 13:28:05,305] [INFO] Running command: blastn -query GCF_019966545.1_ASM1996654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59a5e874-4b3b-46db-88e6-31e742032bb2/dqc_reference/reference_markers.fasta -out GCF_019966545.1_ASM1996654v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:06,189] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:06,192] [INFO] Selected 30 target genomes.
[2024-01-24 13:28:06,193] [INFO] Target genome list was writen to GCF_019966545.1_ASM1996654v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:06,214] [INFO] Task started: fastANI
[2024-01-24 13:28:06,215] [INFO] Running command: fastANI --query /var/lib/cwl/stgfca1887a-d5a0-405b-8522-4a067562a780/GCF_019966545.1_ASM1996654v1_genomic.fna.gz --refList GCF_019966545.1_ASM1996654v1_genomic.fna/target_genomes.txt --output GCF_019966545.1_ASM1996654v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:27,971] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:27,972] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59a5e874-4b3b-46db-88e6-31e742032bb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:27,972] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59a5e874-4b3b-46db-88e6-31e742032bb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:27,997] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:28:27,997] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:28:27,998] [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
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	79.4279	341	1761	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	79.1997	331	1761	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	79.1275	477	1761	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	79.0059	487	1761	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	78.7843	470	1761	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	78.5903	240	1761	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001258055.1	481446	481446	type	True	78.5466	339	1761	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.5268	526	1761	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001404195.1	481446	481446	type	True	78.5223	341	1761	95	below_threshold
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	78.4988	340	1761	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	78.402	447	1761	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.3327	429	1761	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.3271	517	1761	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	78.1559	481	1761	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	78.083	405	1761	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	78.068	391	1761	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	78.0012	282	1761	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	77.7683	356	1761	95	below_threshold
Salinihabitans flavidus	strain=DSM 27842	GCA_900110425.1	569882	569882	type	True	77.685	307	1761	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	77.6673	316	1761	95	below_threshold
Phaeobacter inhibens	strain=DSM 16374	GCA_000473105.1	221822	221822	type	True	77.591	320	1761	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.5771	319	1761	95	below_threshold
Tritonibacter mobilis	strain=NBRC101030	GCA_001681715.1	379347	379347	type	True	77.4831	290	1761	95	below_threshold
Tritonibacter mobilis	strain=DSM 23403	GCA_900106635.1	379347	379347	type	True	77.4449	293	1761	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	77.4012	340	1761	95	below_threshold
Roseivivax halodurans	strain=JCM 10272	GCA_000521785.1	93683	93683	type	True	77.3478	300	1761	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	77.309	292	1761	95	below_threshold
Tritonibacter multivorans	strain=DSM 26470	GCA_900112515.1	928856	928856	type	True	77.2875	291	1761	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.1218	291	1761	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	76.881	243	1761	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:28,001] [INFO] DFAST Taxonomy check result was written to GCF_019966545.1_ASM1996654v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:28,002] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:28,002] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:28,002] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59a5e874-4b3b-46db-88e6-31e742032bb2/dqc_reference/checkm_data
[2024-01-24 13:28:28,003] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:28,062] [INFO] Task started: CheckM
[2024-01-24 13:28:28,063] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019966545.1_ASM1996654v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019966545.1_ASM1996654v1_genomic.fna/checkm_input GCF_019966545.1_ASM1996654v1_genomic.fna/checkm_result
[2024-01-24 13:29:17,645] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:17,647] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:17,668] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:17,669] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:17,669] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019966545.1_ASM1996654v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:17,669] [INFO] Task started: Blastn
[2024-01-24 13:29:17,670] [INFO] Running command: blastn -query GCF_019966545.1_ASM1996654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59a5e874-4b3b-46db-88e6-31e742032bb2/dqc_reference/reference_markers_gtdb.fasta -out GCF_019966545.1_ASM1996654v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:18,961] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:18,966] [INFO] Selected 20 target genomes.
[2024-01-24 13:29:18,966] [INFO] Target genome list was writen to GCF_019966545.1_ASM1996654v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:19,002] [INFO] Task started: fastANI
[2024-01-24 13:29:19,003] [INFO] Running command: fastANI --query /var/lib/cwl/stgfca1887a-d5a0-405b-8522-4a067562a780/GCF_019966545.1_ASM1996654v1_genomic.fna.gz --refList GCF_019966545.1_ASM1996654v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019966545.1_ASM1996654v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:37,456] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:37,478] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:37,479] [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_016758075.1	s__CAU-1492 sp016758075	95.7288	1613	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1492	95.0	99.98	99.98	0.95	0.95	2	conclusive
GCF_002210165.1	s__CAU-1492 sp002210165	91.5117	1510	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1492	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	80.1693	621	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335585.1	s__Sulfitobacter sp003335585	79.8202	581	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003646465.1	s__Chachezhania antarctica	79.631	461	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Chachezhania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938225.1	s__Arenibacterium halophilum	79.5485	672	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Arenibacterium	95.0	96.35	96.35	0.87	0.87	2	-
GCF_003116585.1	s__Albibacillus kandeliae	79.3208	666	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	79.3005	476	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002210095.1	s__Marinibacterium profundimaris	79.0816	559	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	78.5277	527	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656415.1	s__Seohaeicola zhoushanensis	78.5251	596	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Seohaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428585.1	s__Sedimentitalea sp016428585	78.3467	495	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	78.3378	429	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	78.3239	515	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCA_003217735.2	s__Marinibacterium sp003217735	78.2666	516	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_900142665.1	s__Roseovarius pacificus	78.2575	355	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_001679925.1	s__Leisingera sp001679925	78.1607	403	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813965.1	s__Leisingera sp000813965	77.9559	401	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106935.1	s__Sulfitobacter pontiacus	77.6641	317	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_002407245.1	s__Phaeobacter piscinae	77.4121	338	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	97.42	96.04	0.93	0.90	10	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:37,481] [INFO] GTDB search result was written to GCF_019966545.1_ASM1996654v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:37,481] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:37,486] [INFO] DFAST_QC result json was written to GCF_019966545.1_ASM1996654v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:37,486] [INFO] DFAST_QC completed!
[2024-01-24 13:29:37,486] [INFO] Total running time: 0h1m51s