[2024-01-24 12:44:42,183] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:42,186] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:42,186] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf6a8b34-36b3-4485-bcfa-1e42db1fa5f1/dqc_reference
[2024-01-24 12:44:43,531] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:43,532] [INFO] Task started: Prodigal
[2024-01-24 12:44:43,533] [INFO] Running command: gunzip -c /var/lib/cwl/stg99a260dc-48f2-4423-99c8-0672d653161b/GCF_016653255.1_ASM1665325v1_genomic.fna.gz | prodigal -d GCF_016653255.1_ASM1665325v1_genomic.fna/cds.fna -a GCF_016653255.1_ASM1665325v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:53,763] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:53,764] [INFO] Task started: HMMsearch
[2024-01-24 12:44:53,764] [INFO] Running command: hmmsearch --tblout GCF_016653255.1_ASM1665325v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf6a8b34-36b3-4485-bcfa-1e42db1fa5f1/dqc_reference/reference_markers.hmm GCF_016653255.1_ASM1665325v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:54,060] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:54,061] [INFO] Found 6/6 markers.
[2024-01-24 12:44:54,096] [INFO] Query marker FASTA was written to GCF_016653255.1_ASM1665325v1_genomic.fna/markers.fasta
[2024-01-24 12:44:54,097] [INFO] Task started: Blastn
[2024-01-24 12:44:54,097] [INFO] Running command: blastn -query GCF_016653255.1_ASM1665325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf6a8b34-36b3-4485-bcfa-1e42db1fa5f1/dqc_reference/reference_markers.fasta -out GCF_016653255.1_ASM1665325v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:55,317] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:55,321] [INFO] Selected 29 target genomes.
[2024-01-24 12:44:55,322] [INFO] Target genome list was writen to GCF_016653255.1_ASM1665325v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:55,334] [INFO] Task started: fastANI
[2024-01-24 12:44:55,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg99a260dc-48f2-4423-99c8-0672d653161b/GCF_016653255.1_ASM1665325v1_genomic.fna.gz --refList GCF_016653255.1_ASM1665325v1_genomic.fna/target_genomes.txt --output GCF_016653255.1_ASM1665325v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:17,651] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:17,652] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf6a8b34-36b3-4485-bcfa-1e42db1fa5f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:17,653] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf6a8b34-36b3-4485-bcfa-1e42db1fa5f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:17,675] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:45:17,676] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:45:17,676] [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	79.1905	384	1000	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.8971	435	1000	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.7294	390	1000	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.7226	444	1000	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.721	437	1000	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.6878	396	1000	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	78.6463	382	1000	95	below_threshold
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	78.591	392	1000	95	below_threshold
Allgaiera indica	strain=DSM 24802	GCA_900106675.1	765699	765699	type	True	78.5783	389	1000	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	78.5756	352	1000	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	78.5119	359	1000	95	below_threshold
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	78.4734	399	1000	95	below_threshold
Phaeovulum vinaykumarii	strain=DSM 18714	GCA_900156695.1	407234	407234	type	True	78.4701	403	1000	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	78.4542	374	1000	95	below_threshold
Paracoccus sphaerophysae	strain=HAMBI 3106	GCA_000763805.1	690417	690417	type	True	78.3385	374	1000	95	below_threshold
Paracoccus aeridis	strain=JC501	GCA_004923205.2	1966466	1966466	type	True	78.3261	340	1000	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_001720585.1	445629	445629	type	True	78.3183	368	1000	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.2638	413	1000	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_003046325.1	445629	445629	type	True	78.2113	388	1000	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	78.1759	395	1000	95	below_threshold
Paracoccus salipaludis	strain=WN007	GCA_002287065.1	2032623	2032623	type	True	78.1684	360	1000	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	78.1682	337	1000	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.1658	388	1000	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.0861	346	1000	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.8713	365	1000	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.8686	365	1000	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	77.7807	342	1000	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	77.7748	350	1000	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.694	327	1000	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:17,678] [INFO] DFAST Taxonomy check result was written to GCF_016653255.1_ASM1665325v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:17,678] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:17,678] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:17,679] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf6a8b34-36b3-4485-bcfa-1e42db1fa5f1/dqc_reference/checkm_data
[2024-01-24 12:45:17,680] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:17,723] [INFO] Task started: CheckM
[2024-01-24 12:45:17,723] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016653255.1_ASM1665325v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016653255.1_ASM1665325v1_genomic.fna/checkm_input GCF_016653255.1_ASM1665325v1_genomic.fna/checkm_result
[2024-01-24 12:46:00,970] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:00,971] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:00,998] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:00,998] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:00,999] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016653255.1_ASM1665325v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:00,999] [INFO] Task started: Blastn
[2024-01-24 12:46:00,999] [INFO] Running command: blastn -query GCF_016653255.1_ASM1665325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf6a8b34-36b3-4485-bcfa-1e42db1fa5f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_016653255.1_ASM1665325v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:03,094] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:03,100] [INFO] Selected 15 target genomes.
[2024-01-24 12:46:03,100] [INFO] Target genome list was writen to GCF_016653255.1_ASM1665325v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:03,123] [INFO] Task started: fastANI
[2024-01-24 12:46:03,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg99a260dc-48f2-4423-99c8-0672d653161b/GCF_016653255.1_ASM1665325v1_genomic.fna.gz --refList GCF_016653255.1_ASM1665325v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016653255.1_ASM1665325v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:12,320] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:12,334] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:12,335] [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_016653255.1	s__Rhodobaculum claviforme	100.0	986	1000	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_007121055.1	s__Rhodobaculum sp007121055	82.9561	431	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551745.1	s__Rhodobaculum sp003551745	80.4153	380	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126375.1	s__Rhodobaculum sp007126375	80.2145	396	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551925.1	s__PUOA01 sp003551925	79.5158	390	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__PUOA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350345.1	s__Rhodobaculum breve	79.1717	385	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	79.1667	425	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017599285.1	s__Cereibacter_A azotoformans	78.9099	347	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	98.54	95.54	0.92	0.86	6	-
GCA_002967695.1	s__Rhodobaculum sp002967695	78.776	391	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487335.1	s__S012-89 sp015487335	78.7539	268	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__S012-89	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649175.1	s__Rhodovulum strictum	78.7156	445	1000	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	78.7014	439	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007129775.1	s__Rhodobaculum sp007129775	78.6162	313	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007117005.1	s__Pararhodobacter sp007117005	78.3464	312	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	98.98	98.98	0.82	0.82	2	-
GCA_007128865.1	s__Rhodobaculum sp007128865	78.2831	251	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	97.54	97.54	0.66	0.66	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:12,336] [INFO] GTDB search result was written to GCF_016653255.1_ASM1665325v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:12,337] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:12,342] [INFO] DFAST_QC result json was written to GCF_016653255.1_ASM1665325v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:12,342] [INFO] DFAST_QC completed!
[2024-01-24 12:46:12,342] [INFO] Total running time: 0h1m30s