[2024-01-25 19:01:35,915] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:01:35,917] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:01:35,917] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d18336a-c8d4-435e-ab07-29a86e7ebd83/dqc_reference
[2024-01-25 19:01:37,126] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:01:37,127] [INFO] Task started: Prodigal
[2024-01-25 19:01:37,127] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ef26027-93da-4ec6-93e3-b818adb1eb3a/GCF_013093415.1_ASM1309341v1_genomic.fna.gz | prodigal -d GCF_013093415.1_ASM1309341v1_genomic.fna/cds.fna -a GCF_013093415.1_ASM1309341v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:01:46,790] [INFO] Task succeeded: Prodigal
[2024-01-25 19:01:46,791] [INFO] Task started: HMMsearch
[2024-01-25 19:01:46,791] [INFO] Running command: hmmsearch --tblout GCF_013093415.1_ASM1309341v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d18336a-c8d4-435e-ab07-29a86e7ebd83/dqc_reference/reference_markers.hmm GCF_013093415.1_ASM1309341v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:01:47,009] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:01:47,010] [INFO] Found 6/6 markers.
[2024-01-25 19:01:47,040] [INFO] Query marker FASTA was written to GCF_013093415.1_ASM1309341v1_genomic.fna/markers.fasta
[2024-01-25 19:01:47,040] [INFO] Task started: Blastn
[2024-01-25 19:01:47,040] [INFO] Running command: blastn -query GCF_013093415.1_ASM1309341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d18336a-c8d4-435e-ab07-29a86e7ebd83/dqc_reference/reference_markers.fasta -out GCF_013093415.1_ASM1309341v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:48,056] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:48,059] [INFO] Selected 21 target genomes.
[2024-01-25 19:01:48,059] [INFO] Target genome list was writen to GCF_013093415.1_ASM1309341v1_genomic.fna/target_genomes.txt
[2024-01-25 19:01:48,095] [INFO] Task started: fastANI
[2024-01-25 19:01:48,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ef26027-93da-4ec6-93e3-b818adb1eb3a/GCF_013093415.1_ASM1309341v1_genomic.fna.gz --refList GCF_013093415.1_ASM1309341v1_genomic.fna/target_genomes.txt --output GCF_013093415.1_ASM1309341v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:07,520] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:07,520] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d18336a-c8d4-435e-ab07-29a86e7ebd83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:07,520] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d18336a-c8d4-435e-ab07-29a86e7ebd83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:07,533] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:02:07,533] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:02:07,533] [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
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	100.0	1204	1207	95	conclusive
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	81.0666	640	1207	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.8747	440	1207	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.7538	440	1207	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	78.6706	436	1207	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	78.6518	344	1207	95	below_threshold
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	78.5645	368	1207	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.5255	453	1207	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	78.5103	419	1207	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	78.4913	386	1207	95	below_threshold
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	78.4822	382	1207	95	below_threshold
Oceanomicrobium pacificus	strain=KN286	GCA_009833495.1	2692916	2692916	type	True	78.3405	366	1207	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	78.2477	440	1207	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	78.1916	409	1207	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	78.115	398	1207	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	78.1022	366	1207	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.9613	430	1207	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	77.9011	384	1207	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	77.8681	351	1207	95	below_threshold
Amaricoccus macauensis	strain=DSM 101730	GCA_014201905.1	57001	57001	type	True	77.758	316	1207	95	below_threshold
Coraliihabitans acroporae	strain=NNCM2	GCA_019891535.1	2834412	2834412	type	True	77.4182	298	1207	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:02:07,550] [INFO] DFAST Taxonomy check result was written to GCF_013093415.1_ASM1309341v1_genomic.fna/tc_result.tsv
[2024-01-25 19:02:07,551] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:07,551] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:07,551] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d18336a-c8d4-435e-ab07-29a86e7ebd83/dqc_reference/checkm_data
[2024-01-25 19:02:07,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:07,590] [INFO] Task started: CheckM
[2024-01-25 19:02:07,590] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013093415.1_ASM1309341v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013093415.1_ASM1309341v1_genomic.fna/checkm_input GCF_013093415.1_ASM1309341v1_genomic.fna/checkm_result
[2024-01-25 19:02:46,679] [INFO] Task succeeded: CheckM
[2024-01-25 19:02:46,680] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:02:46,693] [INFO] ===== Completeness check finished =====
[2024-01-25 19:02:46,693] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:02:46,694] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013093415.1_ASM1309341v1_genomic.fna/markers.fasta)
[2024-01-25 19:02:46,694] [INFO] Task started: Blastn
[2024-01-25 19:02:46,694] [INFO] Running command: blastn -query GCF_013093415.1_ASM1309341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d18336a-c8d4-435e-ab07-29a86e7ebd83/dqc_reference/reference_markers_gtdb.fasta -out GCF_013093415.1_ASM1309341v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:48,725] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:48,727] [INFO] Selected 19 target genomes.
[2024-01-25 19:02:48,728] [INFO] Target genome list was writen to GCF_013093415.1_ASM1309341v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:02:48,752] [INFO] Task started: fastANI
[2024-01-25 19:02:48,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ef26027-93da-4ec6-93e3-b818adb1eb3a/GCF_013093415.1_ASM1309341v1_genomic.fna.gz --refList GCF_013093415.1_ASM1309341v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013093415.1_ASM1309341v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:03:04,174] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:04,186] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:03:04,187] [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_013093415.1	s__Halovulum dunhuangense	100.0	1204	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009697225.1	s__Halovulum marinum	81.0793	638	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003265325.1	s__Halovulum sediminis	79.974	642	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	79.3496	483	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649175.1	s__Rhodovulum strictum	78.7454	443	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	78.5134	455	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887635.2	s__Paroceanicella profunda	78.5038	419	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797755.1	s__Brevirhabdus pacifica	78.4827	387	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	-
GCF_900156695.1	s__Bieblia_A vinaykumarii	78.4688	369	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Bieblia_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003511785.1	s__UBA7951 sp003511785	78.4086	304	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009833495.1	s__Oceanomicrobium pacificus	78.3611	364	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	78.3544	391	1207	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_001620265.1	s__Frigidibacter mobilis	78.2594	438	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226775.1	s__Marinovum sp006226775	78.2381	444	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385685.1	s__Amaricoccus solimangrovi	78.218	407	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100085.1	s__Salipiger marinus	77.9754	430	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_000473145.1	s__Leisingera daeponensis	77.8641	352	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.26	98.26	0.94	0.94	2	-
GCF_014201905.1	s__Amaricoccus macauensis	77.7625	315	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003258405.1	s__Amaricoccus sp003258405	77.7371	340	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:03:04,188] [INFO] GTDB search result was written to GCF_013093415.1_ASM1309341v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:03:04,188] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:03:04,194] [INFO] DFAST_QC result json was written to GCF_013093415.1_ASM1309341v1_genomic.fna/dqc_result.json
[2024-01-25 19:03:04,195] [INFO] DFAST_QC completed!
[2024-01-25 19:03:04,195] [INFO] Total running time: 0h1m28s