[2024-01-25 17:45:05,525] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:45:05,527] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:45:05,527] [INFO] DQC Reference Directory: /var/lib/cwl/stg538e159c-c6d6-4c2d-a61e-2eff231e5e4a/dqc_reference
[2024-01-25 17:45:06,706] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:45:06,707] [INFO] Task started: Prodigal
[2024-01-25 17:45:06,708] [INFO] Running command: gunzip -c /var/lib/cwl/stg324ecc9f-581d-473b-acf0-9ccb217945e9/GCF_003350345.1_ASM335034v1_genomic.fna.gz | prodigal -d GCF_003350345.1_ASM335034v1_genomic.fna/cds.fna -a GCF_003350345.1_ASM335034v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:45:16,722] [INFO] Task succeeded: Prodigal
[2024-01-25 17:45:16,723] [INFO] Task started: HMMsearch
[2024-01-25 17:45:16,723] [INFO] Running command: hmmsearch --tblout GCF_003350345.1_ASM335034v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg538e159c-c6d6-4c2d-a61e-2eff231e5e4a/dqc_reference/reference_markers.hmm GCF_003350345.1_ASM335034v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:45:16,950] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:45:16,951] [INFO] Found 6/6 markers.
[2024-01-25 17:45:16,982] [INFO] Query marker FASTA was written to GCF_003350345.1_ASM335034v1_genomic.fna/markers.fasta
[2024-01-25 17:45:16,982] [INFO] Task started: Blastn
[2024-01-25 17:45:16,982] [INFO] Running command: blastn -query GCF_003350345.1_ASM335034v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg538e159c-c6d6-4c2d-a61e-2eff231e5e4a/dqc_reference/reference_markers.fasta -out GCF_003350345.1_ASM335034v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:17,930] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:17,934] [INFO] Selected 25 target genomes.
[2024-01-25 17:45:17,934] [INFO] Target genome list was writen to GCF_003350345.1_ASM335034v1_genomic.fna/target_genomes.txt
[2024-01-25 17:45:17,962] [INFO] Task started: fastANI
[2024-01-25 17:45:17,962] [INFO] Running command: fastANI --query /var/lib/cwl/stg324ecc9f-581d-473b-acf0-9ccb217945e9/GCF_003350345.1_ASM335034v1_genomic.fna.gz --refList GCF_003350345.1_ASM335034v1_genomic.fna/target_genomes.txt --output GCF_003350345.1_ASM335034v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:45:35,889] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:35,890] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg538e159c-c6d6-4c2d-a61e-2eff231e5e4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:45:35,890] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg538e159c-c6d6-4c2d-a61e-2eff231e5e4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:45:35,904] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:45:35,904] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:45:35,904] [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
Alkalilacustris brevis	strain=34079	GCA_003350345.1	2026338	2026338	type	True	100.0	1106	1107	95	conclusive
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	79.0312	430	1107	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	78.8857	420	1107	95	below_threshold
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	78.8495	417	1107	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.8109	436	1107	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.7564	414	1107	95	below_threshold
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	78.5461	398	1107	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	78.5205	397	1107	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.5136	384	1107	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_000520135.2	35806	35806	type	True	78.503	398	1107	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	78.4335	292	1107	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	78.393	315	1107	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_008824185.1	82367	82367	type	True	78.3391	361	1107	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	78.2888	372	1107	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	78.2784	371	1107	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.2433	338	1107	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.1739	363	1107	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	78.1014	342	1107	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.9707	355	1107	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.9702	355	1107	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	77.8616	330	1107	95	below_threshold
Roseicitreum antarcticum	strain=ZS2-28	GCA_014681765.1	564137	564137	type	True	77.7479	356	1107	95	below_threshold
Roseicitreum antarcticum	strain=CGMCC 1.8894	GCA_900107025.1	564137	564137	type	True	77.7063	344	1107	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	77.4493	248	1107	95	below_threshold
Silicimonas algicola	strain=KC90	GCA_003970735.1	1826607	1826607	type	True	77.4228	254	1107	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:45:35,905] [INFO] DFAST Taxonomy check result was written to GCF_003350345.1_ASM335034v1_genomic.fna/tc_result.tsv
[2024-01-25 17:45:35,906] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:45:35,906] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:45:35,906] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg538e159c-c6d6-4c2d-a61e-2eff231e5e4a/dqc_reference/checkm_data
[2024-01-25 17:45:35,907] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:45:35,943] [INFO] Task started: CheckM
[2024-01-25 17:45:35,943] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003350345.1_ASM335034v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003350345.1_ASM335034v1_genomic.fna/checkm_input GCF_003350345.1_ASM335034v1_genomic.fna/checkm_result
[2024-01-25 17:46:12,826] [INFO] Task succeeded: CheckM
[2024-01-25 17:46:12,827] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:46:12,847] [INFO] ===== Completeness check finished =====
[2024-01-25 17:46:12,847] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:46:12,848] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003350345.1_ASM335034v1_genomic.fna/markers.fasta)
[2024-01-25 17:46:12,848] [INFO] Task started: Blastn
[2024-01-25 17:46:12,848] [INFO] Running command: blastn -query GCF_003350345.1_ASM335034v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg538e159c-c6d6-4c2d-a61e-2eff231e5e4a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003350345.1_ASM335034v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:14,847] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:14,850] [INFO] Selected 21 target genomes.
[2024-01-25 17:46:14,850] [INFO] Target genome list was writen to GCF_003350345.1_ASM335034v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:46:14,879] [INFO] Task started: fastANI
[2024-01-25 17:46:14,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg324ecc9f-581d-473b-acf0-9ccb217945e9/GCF_003350345.1_ASM335034v1_genomic.fna.gz --refList GCF_003350345.1_ASM335034v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003350345.1_ASM335034v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:46:29,444] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:29,458] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:46:29,458] [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_003350345.1	s__Rhodobaculum breve	100.0	1106	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003558415.1	s__Rhodobaculum sp003558415	80.1513	312	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002967695.1	s__Rhodobaculum sp002967695	79.2945	455	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653255.1	s__Rhodobaculum claviforme	79.1488	384	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007129775.1	s__Rhodobaculum sp007129775	78.9535	338	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	78.8307	434	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003564655.1	s__Roseinatronobacter sp003564655	78.7086	321	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003561595.1	s__Roseinatronobacter sp003561595	78.692	304	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	98.99	98.90	0.87	0.78	5	-
GCA_007131945.1	s__Pararhodobacter sp007131945	78.6611	364	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	99.16	99.15	0.86	0.82	3	-
GCA_003550665.1	s__Rhodobaculum sp003550665	78.6492	337	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	99.32	99.19	0.86	0.85	4	-
GCA_003551745.1	s__Rhodobaculum sp003551745	78.6319	298	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196965.1	s__Actibacterium_A naphthalenivorans	78.5936	368	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium_A	95.0	98.28	97.38	0.93	0.89	4	-
GCF_900106675.1	s__Acidimangrovimonas indica	78.5697	400	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Acidimangrovimonas	95.0	99.99	99.99	1.00	0.99	3	-
GCA_007131685.1	s__Rhodobaculum sp007131685	78.5441	331	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	99.44	99.41	0.86	0.86	3	-
GCA_014359745.1	s__JACIYW01 sp014359745	78.5035	323	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JACIYW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007128865.1	s__Rhodobaculum sp007128865	78.4228	260	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	97.54	97.54	0.66	0.66	2	-
GCF_002797755.1	s__Brevirhabdus pacifica	78.3802	316	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	-
GCF_008824185.1	s__Paracoccus pantotrophus	78.3383	361	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.22	98.98	0.90	0.84	8	-
GCF_019104745.1	s__CAU-1522 sp019104745	78.3294	341	1107	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_000763885.1	s__Paracoccus versutus	78.2983	369	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	98.67	98.17	0.87	0.76	7	-
GCF_003344785.1	s__Puniceibacterium profundi	78.1261	351	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:46:29,459] [INFO] GTDB search result was written to GCF_003350345.1_ASM335034v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:46:29,460] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:46:29,463] [INFO] DFAST_QC result json was written to GCF_003350345.1_ASM335034v1_genomic.fna/dqc_result.json
[2024-01-25 17:46:29,464] [INFO] DFAST_QC completed!
[2024-01-25 17:46:29,464] [INFO] Total running time: 0h1m24s