[2024-01-24 12:06:10,393] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:10,396] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:10,396] [INFO] DQC Reference Directory: /var/lib/cwl/stg57e99b7d-302a-4075-88ac-153e31f593f2/dqc_reference
[2024-01-24 12:06:13,247] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:13,250] [INFO] Task started: Prodigal
[2024-01-24 12:06:13,250] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0ad155b-08cf-46a2-9561-6a15abed260f/GCF_017813235.1_ASM1781323v1_genomic.fna.gz | prodigal -d GCF_017813235.1_ASM1781323v1_genomic.fna/cds.fna -a GCF_017813235.1_ASM1781323v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:28,356] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:28,356] [INFO] Task started: HMMsearch
[2024-01-24 12:06:28,356] [INFO] Running command: hmmsearch --tblout GCF_017813235.1_ASM1781323v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57e99b7d-302a-4075-88ac-153e31f593f2/dqc_reference/reference_markers.hmm GCF_017813235.1_ASM1781323v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:28,726] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:28,727] [INFO] Found 6/6 markers.
[2024-01-24 12:06:28,777] [INFO] Query marker FASTA was written to GCF_017813235.1_ASM1781323v1_genomic.fna/markers.fasta
[2024-01-24 12:06:28,777] [INFO] Task started: Blastn
[2024-01-24 12:06:28,778] [INFO] Running command: blastn -query GCF_017813235.1_ASM1781323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57e99b7d-302a-4075-88ac-153e31f593f2/dqc_reference/reference_markers.fasta -out GCF_017813235.1_ASM1781323v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:29,720] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:29,724] [INFO] Selected 22 target genomes.
[2024-01-24 12:06:29,724] [INFO] Target genome list was writen to GCF_017813235.1_ASM1781323v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:29,731] [INFO] Task started: fastANI
[2024-01-24 12:06:29,732] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0ad155b-08cf-46a2-9561-6a15abed260f/GCF_017813235.1_ASM1781323v1_genomic.fna.gz --refList GCF_017813235.1_ASM1781323v1_genomic.fna/target_genomes.txt --output GCF_017813235.1_ASM1781323v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:50,240] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:50,240] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57e99b7d-302a-4075-88ac-153e31f593f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:50,241] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57e99b7d-302a-4075-88ac-153e31f593f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:50,260] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:06:50,260] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:06:50,260] [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
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	79.2598	683	1572	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	79.1659	716	1572	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	79.1322	716	1572	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	78.8179	588	1572	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	78.7703	600	1572	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	78.7403	579	1572	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	78.7278	611	1572	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	78.7012	608	1572	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	78.6807	575	1572	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	78.5907	495	1572	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.327	592	1572	95	below_threshold
Roseivivax marinus	strain=DSM 27511	GCA_900109705.1	1379903	1379903	type	True	78.3004	457	1572	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.269	530	1572	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.2284	478	1572	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	78.1259	474	1572	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	78.1103	475	1572	95	below_threshold
Roseivivax halodurans	strain=JCM 10272	GCA_000521785.1	93683	93683	type	True	77.9942	412	1572	95	below_threshold
Roseivivax jejudonensis	strain=CECT 8625	GCA_900172265.1	1529041	1529041	type	True	77.939	451	1572	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	77.903	386	1572	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.7774	429	1572	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.4278	371	1572	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.5718	213	1572	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:50,262] [INFO] DFAST Taxonomy check result was written to GCF_017813235.1_ASM1781323v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:50,263] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:50,263] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:50,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57e99b7d-302a-4075-88ac-153e31f593f2/dqc_reference/checkm_data
[2024-01-24 12:06:50,265] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:50,314] [INFO] Task started: CheckM
[2024-01-24 12:06:50,314] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017813235.1_ASM1781323v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017813235.1_ASM1781323v1_genomic.fna/checkm_input GCF_017813235.1_ASM1781323v1_genomic.fna/checkm_result
[2024-01-24 12:07:36,386] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:36,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:36,413] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:36,413] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:36,414] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017813235.1_ASM1781323v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:36,414] [INFO] Task started: Blastn
[2024-01-24 12:07:36,414] [INFO] Running command: blastn -query GCF_017813235.1_ASM1781323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57e99b7d-302a-4075-88ac-153e31f593f2/dqc_reference/reference_markers_gtdb.fasta -out GCF_017813235.1_ASM1781323v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:37,912] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:37,917] [INFO] Selected 16 target genomes.
[2024-01-24 12:07:37,917] [INFO] Target genome list was writen to GCF_017813235.1_ASM1781323v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:37,937] [INFO] Task started: fastANI
[2024-01-24 12:07:37,937] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0ad155b-08cf-46a2-9561-6a15abed260f/GCF_017813235.1_ASM1781323v1_genomic.fna.gz --refList GCF_017813235.1_ASM1781323v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017813235.1_ASM1781323v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:54,021] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:54,038] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:54,038] [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_017813235.1	s__Sagittula sp017813235	100.0	1571	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002814095.1	s__Sagittula sp002814095	80.8313	959	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169415.1	s__Sagittula stellata	80.3248	832	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255395.1	s__AWRV01 sp017255395	79.8709	737	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016806125.1	s__AWRV01 sp000504185	79.8547	727	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	99.97	99.97	1.00	1.00	2	-
GCF_003667315.2	s__Tropicibacter sp003667315	79.3068	675	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196795.1	s__Sagittula marina	79.2701	681	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	79.2573	695	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101505.1	s__Mameliella alba	79.1251	717	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCA_019218285.1	s__DP3N28-2 sp019218285	78.7251	581	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__DP3N28-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	78.5616	566	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100085.1	s__Salipiger marinus	78.3361	590	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_000521865.1	s__Roseivivax isoporae	78.271	529	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	78.2426	449	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	78.1207	474	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	77.777	429	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:54,040] [INFO] GTDB search result was written to GCF_017813235.1_ASM1781323v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:54,041] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:54,050] [INFO] DFAST_QC result json was written to GCF_017813235.1_ASM1781323v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:54,050] [INFO] DFAST_QC completed!
[2024-01-24 12:07:54,050] [INFO] Total running time: 0h1m44s