[2024-01-25 18:06:20,767] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:20,768] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:20,768] [INFO] DQC Reference Directory: /var/lib/cwl/stg2db81205-5b74-4c19-9b54-e5b8dcf2d431/dqc_reference
[2024-01-25 18:06:21,947] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:21,948] [INFO] Task started: Prodigal
[2024-01-25 18:06:21,948] [INFO] Running command: gunzip -c /var/lib/cwl/stg2addeb2f-f405-4cce-83e4-27e7480ccb36/GCF_030848945.1_ASM3084894v1_genomic.fna.gz | prodigal -d GCF_030848945.1_ASM3084894v1_genomic.fna/cds.fna -a GCF_030848945.1_ASM3084894v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:33,939] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:33,940] [INFO] Task started: HMMsearch
[2024-01-25 18:06:33,940] [INFO] Running command: hmmsearch --tblout GCF_030848945.1_ASM3084894v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2db81205-5b74-4c19-9b54-e5b8dcf2d431/dqc_reference/reference_markers.hmm GCF_030848945.1_ASM3084894v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:34,221] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:34,226] [INFO] Found 6/6 markers.
[2024-01-25 18:06:34,267] [INFO] Query marker FASTA was written to GCF_030848945.1_ASM3084894v1_genomic.fna/markers.fasta
[2024-01-25 18:06:34,267] [INFO] Task started: Blastn
[2024-01-25 18:06:34,267] [INFO] Running command: blastn -query GCF_030848945.1_ASM3084894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2db81205-5b74-4c19-9b54-e5b8dcf2d431/dqc_reference/reference_markers.fasta -out GCF_030848945.1_ASM3084894v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:35,114] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:35,117] [INFO] Selected 27 target genomes.
[2024-01-25 18:06:35,117] [INFO] Target genome list was writen to GCF_030848945.1_ASM3084894v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:35,147] [INFO] Task started: fastANI
[2024-01-25 18:06:35,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg2addeb2f-f405-4cce-83e4-27e7480ccb36/GCF_030848945.1_ASM3084894v1_genomic.fna.gz --refList GCF_030848945.1_ASM3084894v1_genomic.fna/target_genomes.txt --output GCF_030848945.1_ASM3084894v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:56,080] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:56,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2db81205-5b74-4c19-9b54-e5b8dcf2d431/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:56,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2db81205-5b74-4c19-9b54-e5b8dcf2d431/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:56,099] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:06:56,099] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:06:56,099] [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
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	79.0434	517	1451	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	79.0206	526	1451	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.7817	554	1451	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.7794	595	1451	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	78.6945	537	1451	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	78.6134	494	1451	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	78.5252	494	1451	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	78.434	520	1451	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	78.4241	525	1451	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	78.3947	523	1451	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	78.3773	485	1451	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	78.3357	484	1451	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	78.1213	437	1451	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.103	480	1451	95	below_threshold
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	78.074	463	1451	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.0491	378	1451	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.0283	387	1451	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	77.9884	333	1451	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	77.9789	416	1451	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	77.8663	487	1451	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	77.8632	486	1451	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	77.714	396	1451	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.5511	333	1451	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	77.526	346	1451	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.4734	316	1451	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.3453	277	1451	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.6469	241	1451	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:56,101] [INFO] DFAST Taxonomy check result was written to GCF_030848945.1_ASM3084894v1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:56,102] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:56,102] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:56,103] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2db81205-5b74-4c19-9b54-e5b8dcf2d431/dqc_reference/checkm_data
[2024-01-25 18:06:56,104] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:56,146] [INFO] Task started: CheckM
[2024-01-25 18:06:56,146] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030848945.1_ASM3084894v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030848945.1_ASM3084894v1_genomic.fna/checkm_input GCF_030848945.1_ASM3084894v1_genomic.fna/checkm_result
[2024-01-25 18:07:32,314] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:32,315] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:32,333] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:32,333] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:32,334] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030848945.1_ASM3084894v1_genomic.fna/markers.fasta)
[2024-01-25 18:07:32,334] [INFO] Task started: Blastn
[2024-01-25 18:07:32,334] [INFO] Running command: blastn -query GCF_030848945.1_ASM3084894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2db81205-5b74-4c19-9b54-e5b8dcf2d431/dqc_reference/reference_markers_gtdb.fasta -out GCF_030848945.1_ASM3084894v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:33,891] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:33,894] [INFO] Selected 23 target genomes.
[2024-01-25 18:07:33,894] [INFO] Target genome list was writen to GCF_030848945.1_ASM3084894v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:33,928] [INFO] Task started: fastANI
[2024-01-25 18:07:33,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg2addeb2f-f405-4cce-83e4-27e7480ccb36/GCF_030848945.1_ASM3084894v1_genomic.fna.gz --refList GCF_030848945.1_ASM3084894v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030848945.1_ASM3084894v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:53,459] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:53,473] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:07:53,473] [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_005434965.1	s__Marimonas lutisalis	81.1161	859	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389685.1	s__Aquicoccus sp011389685	79.767	611	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aquicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369105.1	s__Aquicoccus porphyridii	79.7441	657	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aquicoccus	95.0	99.99	99.99	1.00	1.00	2	-
GCA_001314705.1	s__Aquicoccus sp001314705	79.4182	619	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aquicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	79.051	522	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900142185.1	s__Lutimaribacter pacificus	78.9938	603	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009857745.1	s__Thalassobius mangrovi	78.7828	594	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	78.77	556	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	78.742	496	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	78.7141	512	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018219815.1	s__Thalassobius aquimarinus	78.6831	539	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	78.6215	493	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	78.521	495	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285435.1	s__Actibacterium ureilyticum	78.4202	436	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	78.4176	505	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728195.1	s__Roseovarius indicus	78.4115	526	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_005938215.1	s__Ruegeria sediminis	78.3851	484	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153725.1	s__Salipiger bermudensis	78.3519	482	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_000152725.1	s__Pseudooceanicola batsensis	78.159	413	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227805.1	s__Aestuariivita sp006227805	78.159	338	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002917925.1	s__Roseovarius confluentis	78.1301	435	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.93	0.93	2	-
GCF_016428585.1	s__Sedimentitalea sp016428585	78.1269	451	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009762325.1	s__Roseovarius faecimaris	78.1135	438	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:53,476] [INFO] GTDB search result was written to GCF_030848945.1_ASM3084894v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:53,479] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:53,486] [INFO] DFAST_QC result json was written to GCF_030848945.1_ASM3084894v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:53,486] [INFO] DFAST_QC completed!
[2024-01-25 18:07:53,486] [INFO] Total running time: 0h1m33s