[2024-01-24 11:35:23,633] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:23,636] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:23,637] [INFO] DQC Reference Directory: /var/lib/cwl/stg47b6b9de-eaa9-4fa0-a51c-5dab5def0aaf/dqc_reference
[2024-01-24 11:35:26,239] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,244] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,245] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe0d53ce-52a0-4bfc-bd36-9f4ed133af73/GCF_019104745.1_ASM1910474v1_genomic.fna.gz | prodigal -d GCF_019104745.1_ASM1910474v1_genomic.fna/cds.fna -a GCF_019104745.1_ASM1910474v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:37,936] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:37,936] [INFO] Task started: HMMsearch
[2024-01-24 11:35:37,936] [INFO] Running command: hmmsearch --tblout GCF_019104745.1_ASM1910474v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47b6b9de-eaa9-4fa0-a51c-5dab5def0aaf/dqc_reference/reference_markers.hmm GCF_019104745.1_ASM1910474v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:38,243] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:38,244] [INFO] Found 6/6 markers.
[2024-01-24 11:35:38,282] [INFO] Query marker FASTA was written to GCF_019104745.1_ASM1910474v1_genomic.fna/markers.fasta
[2024-01-24 11:35:38,282] [INFO] Task started: Blastn
[2024-01-24 11:35:38,283] [INFO] Running command: blastn -query GCF_019104745.1_ASM1910474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47b6b9de-eaa9-4fa0-a51c-5dab5def0aaf/dqc_reference/reference_markers.fasta -out GCF_019104745.1_ASM1910474v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:39,264] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:39,267] [INFO] Selected 28 target genomes.
[2024-01-24 11:35:39,268] [INFO] Target genome list was writen to GCF_019104745.1_ASM1910474v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:39,285] [INFO] Task started: fastANI
[2024-01-24 11:35:39,286] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe0d53ce-52a0-4bfc-bd36-9f4ed133af73/GCF_019104745.1_ASM1910474v1_genomic.fna.gz --refList GCF_019104745.1_ASM1910474v1_genomic.fna/target_genomes.txt --output GCF_019104745.1_ASM1910474v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:01,775] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:01,776] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47b6b9de-eaa9-4fa0-a51c-5dab5def0aaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:01,777] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47b6b9de-eaa9-4fa0-a51c-5dab5def0aaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:01,810] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:36:01,810] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:36:01,811] [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
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	79.9613	695	1233	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	79.9513	703	1233	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	79.7695	614	1233	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	79.7691	609	1233	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	79.5124	619	1233	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	79.47	571	1233	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	79.4003	573	1233	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	79.386	617	1233	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	79.3786	560	1233	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	79.2236	542	1233	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	79.2203	529	1233	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	79.189	531	1233	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	79.1125	474	1233	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	79.0631	584	1233	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	79.0208	586	1233	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	79.0157	549	1233	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.9797	486	1233	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.7804	497	1233	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.7651	458	1233	95	below_threshold
Marivita geojedonensis	strain=DSM 29432	GCA_003002975.1	1123756	1123756	type	True	78.5572	488	1233	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.5497	479	1233	95	below_threshold
Marivita geojedonensis	strain=DPG-138	GCA_002115805.1	1123756	1123756	type	True	78.5235	491	1233	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.2155	362	1233	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.1389	469	1233	95	below_threshold
Alkalilacustris brevis	strain=34079	GCA_003350345.1	2026338	2026338	type	True	78.1235	356	1233	95	below_threshold
Marivita cryptomonadis	strain=CL-SK44	GCA_002115725.1	505252	505252	type	True	78.115	445	1233	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.0761	470	1233	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	78.0753	392	1233	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:01,813] [INFO] DFAST Taxonomy check result was written to GCF_019104745.1_ASM1910474v1_genomic.fna/tc_result.tsv
[2024-01-24 11:36:01,814] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:01,815] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:01,815] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47b6b9de-eaa9-4fa0-a51c-5dab5def0aaf/dqc_reference/checkm_data
[2024-01-24 11:36:01,817] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:01,859] [INFO] Task started: CheckM
[2024-01-24 11:36:01,859] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019104745.1_ASM1910474v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019104745.1_ASM1910474v1_genomic.fna/checkm_input GCF_019104745.1_ASM1910474v1_genomic.fna/checkm_result
[2024-01-24 11:36:44,037] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:44,039] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:44,058] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:44,059] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:44,059] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019104745.1_ASM1910474v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:44,059] [INFO] Task started: Blastn
[2024-01-24 11:36:44,060] [INFO] Running command: blastn -query GCF_019104745.1_ASM1910474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47b6b9de-eaa9-4fa0-a51c-5dab5def0aaf/dqc_reference/reference_markers_gtdb.fasta -out GCF_019104745.1_ASM1910474v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:45,779] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:45,783] [INFO] Selected 26 target genomes.
[2024-01-24 11:36:45,783] [INFO] Target genome list was writen to GCF_019104745.1_ASM1910474v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:45,812] [INFO] Task started: fastANI
[2024-01-24 11:36:45,812] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe0d53ce-52a0-4bfc-bd36-9f4ed133af73/GCF_019104745.1_ASM1910474v1_genomic.fna.gz --refList GCF_019104745.1_ASM1910474v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019104745.1_ASM1910474v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:07,801] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:07,825] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:07,825] [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_019104745.1	s__CAU-1522 sp019104745	100.0	1232	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001482405.1	s__Ponticoccus marisrubri	80.7791	751	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184945.1	s__Maliponia aquimaris	80.7497	793	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maliponia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	80.7345	764	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344785.1	s__Puniceibacterium profundi	80.2323	683	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107235.1	s__Citreimonas salinaria	80.203	594	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	80.1845	613	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900101505.1	s__Mameliella alba	79.9441	704	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCF_001975705.1	s__Salipiger abyssi	79.8365	649	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226775.1	s__Marinovum sp006226775	79.8019	609	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	79.7311	618	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000442255.1	s__Salipiger mucosus	79.633	620	1233	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	79.5239	618	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_009857745.1	s__Thalassobius mangrovi	79.4775	569	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002300555.1	s__Salipiger sp002300555	79.4719	438	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637725.1	s__Marivita lacus	79.4003	573	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	79.2498	538	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227805.1	s__Aestuariivita sp006227805	79.2356	394	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	79.0846	477	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428585.1	s__Sedimentitalea sp016428585	79.0546	527	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116195.1	s__Salipiger pacificus	79.044	583	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.99	99.99	1.00	1.00	2	-
GCA_011048875.1	s__Rhodovulum sp011048875	78.9829	355	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342445.1	s__Rhodovulum euryhalinum	78.8101	493	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115805.1	s__Marivita geojedonensis	78.5319	490	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	100.00	100.00	0.99	0.99	2	-
GCA_016125575.1	s__JAACUH01 sp016125575	78.4496	434	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAACUH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	78.083	469	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:07,827] [INFO] GTDB search result was written to GCF_019104745.1_ASM1910474v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:07,828] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:07,833] [INFO] DFAST_QC result json was written to GCF_019104745.1_ASM1910474v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:07,833] [INFO] DFAST_QC completed!
[2024-01-24 11:37:07,833] [INFO] Total running time: 0h1m44s