[2024-01-24 13:01:26,346] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:26,348] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:26,348] [INFO] DQC Reference Directory: /var/lib/cwl/stg3128e812-0363-4f8a-ae3d-a8e58ab7a79b/dqc_reference
[2024-01-24 13:01:27,708] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:27,709] [INFO] Task started: Prodigal
[2024-01-24 13:01:27,709] [INFO] Running command: gunzip -c /var/lib/cwl/stg51000a71-aeba-4467-9b93-ae13b2db79e7/GCF_020103695.1_ASM2010369v1_genomic.fna.gz | prodigal -d GCF_020103695.1_ASM2010369v1_genomic.fna/cds.fna -a GCF_020103695.1_ASM2010369v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:17,854] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:17,855] [INFO] Task started: HMMsearch
[2024-01-24 13:02:17,855] [INFO] Running command: hmmsearch --tblout GCF_020103695.1_ASM2010369v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3128e812-0363-4f8a-ae3d-a8e58ab7a79b/dqc_reference/reference_markers.hmm GCF_020103695.1_ASM2010369v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:18,328] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:18,329] [INFO] Found 6/6 markers.
[2024-01-24 13:02:18,420] [INFO] Query marker FASTA was written to GCF_020103695.1_ASM2010369v1_genomic.fna/markers.fasta
[2024-01-24 13:02:18,421] [INFO] Task started: Blastn
[2024-01-24 13:02:18,421] [INFO] Running command: blastn -query GCF_020103695.1_ASM2010369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3128e812-0363-4f8a-ae3d-a8e58ab7a79b/dqc_reference/reference_markers.fasta -out GCF_020103695.1_ASM2010369v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:19,186] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:19,191] [INFO] Selected 21 target genomes.
[2024-01-24 13:02:19,191] [INFO] Target genome list was writen to GCF_020103695.1_ASM2010369v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:19,203] [INFO] Task started: fastANI
[2024-01-24 13:02:19,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg51000a71-aeba-4467-9b93-ae13b2db79e7/GCF_020103695.1_ASM2010369v1_genomic.fna.gz --refList GCF_020103695.1_ASM2010369v1_genomic.fna/target_genomes.txt --output GCF_020103695.1_ASM2010369v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:59,302] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:59,302] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3128e812-0363-4f8a-ae3d-a8e58ab7a79b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:59,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3128e812-0363-4f8a-ae3d-a8e58ab7a79b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:59,320] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:02:59,321] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:02:59,321] [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
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	82.0338	1867	4477	95	below_threshold
Stigmatella hybrida	strain=DSM 14722	GCA_020103775.1	394097	394097	type	True	81.8946	1874	4477	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	81.8752	1896	4477	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	80.2696	1783	4477	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	80.2255	1771	4477	95	below_threshold
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	80.2075	1702	4477	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	80.1755	1701	4477	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	80.1665	1762	4477	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_001027285.1	48	48	type	True	80.1628	1778	4477	95	below_threshold
Myxococcus vastator	strain=AM301	GCA_010894475.1	2709664	2709664	type	True	80.1542	1219	4477	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	80.0509	1428	4477	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	80.0399	1449	4477	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	80.0132	1371	4477	95	below_threshold
Corallococcus carmarthensis	strain=CA043D	GCA_003611695.1	2316728	2316728	type	True	79.9052	1449	4477	95	below_threshold
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	79.8859	1401	4477	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	75.1499	133	4477	95	below_threshold
Lujinxingia vulgaris	strain=TMQ4	GCA_007997015.1	2600176	2600176	type	True	74.9962	123	4477	95	below_threshold
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	74.9375	322	4477	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	74.9046	274	4477	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	74.7433	101	4477	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	74.7207	100	4477	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:59,322] [INFO] DFAST Taxonomy check result was written to GCF_020103695.1_ASM2010369v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:59,323] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:59,323] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:59,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3128e812-0363-4f8a-ae3d-a8e58ab7a79b/dqc_reference/checkm_data
[2024-01-24 13:02:59,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:59,439] [INFO] Task started: CheckM
[2024-01-24 13:02:59,439] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020103695.1_ASM2010369v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020103695.1_ASM2010369v1_genomic.fna/checkm_input GCF_020103695.1_ASM2010369v1_genomic.fna/checkm_result
[2024-01-24 13:06:36,553] [INFO] Task succeeded: CheckM
[2024-01-24 13:06:36,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:06:36,583] [INFO] ===== Completeness check finished =====
[2024-01-24 13:06:36,584] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:06:36,584] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020103695.1_ASM2010369v1_genomic.fna/markers.fasta)
[2024-01-24 13:06:36,584] [INFO] Task started: Blastn
[2024-01-24 13:06:36,585] [INFO] Running command: blastn -query GCF_020103695.1_ASM2010369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3128e812-0363-4f8a-ae3d-a8e58ab7a79b/dqc_reference/reference_markers_gtdb.fasta -out GCF_020103695.1_ASM2010369v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:06:37,921] [INFO] Task succeeded: Blastn
[2024-01-24 13:06:37,925] [INFO] Selected 11 target genomes.
[2024-01-24 13:06:37,926] [INFO] Target genome list was writen to GCF_020103695.1_ASM2010369v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:06:37,982] [INFO] Task started: fastANI
[2024-01-24 13:06:37,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg51000a71-aeba-4467-9b93-ae13b2db79e7/GCF_020103695.1_ASM2010369v1_genomic.fna.gz --refList GCF_020103695.1_ASM2010369v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020103695.1_ASM2010369v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:07:08,343] [INFO] Task succeeded: fastANI
[2024-01-24 13:07:08,369] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:07:08,370] [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
GCA_016926755.1	s__Hyalangium sp016926755	84.3524	2070	4477	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Hyalangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737315.1	s__Hyalangium minutum	83.9702	2538	4477	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Hyalangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111745.1	s__Stigmatella erecta	82.0368	1867	4477	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Stigmatella	95.281	N/A	N/A	N/A	N/A	1	-
GCF_900109545.1	s__Stigmatella aurantiaca	81.8932	1890	4477	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Stigmatella	95.281	N/A	N/A	N/A	N/A	1	-
GCF_000165485.1	s__Stigmatella aurantiaca_A	81.6606	1829	4477	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Stigmatella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003044305.1	s__Archangium sp003044305	80.4608	1860	4477	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016887565.1	s__Archangium violaceum_B	80.395	1847	4477	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017301735.1	s__Myxococcus sp017301735	80.2537	1764	4477	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010894435.1	s__Myxococcus trucidator	80.2209	1772	4477	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656495.1	s__Myxococcus sp014656495	80.212	1375	4477	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000733295.1	s__Archangium violaceum	80.204	1704	4477	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	95.60	95.60	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:07:08,372] [INFO] GTDB search result was written to GCF_020103695.1_ASM2010369v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:07:08,372] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:07:08,376] [INFO] DFAST_QC result json was written to GCF_020103695.1_ASM2010369v1_genomic.fna/dqc_result.json
[2024-01-24 13:07:08,376] [INFO] DFAST_QC completed!
[2024-01-24 13:07:08,376] [INFO] Total running time: 0h5m42s