[2024-01-24 14:19:59,699] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:59,701] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:59,701] [INFO] DQC Reference Directory: /var/lib/cwl/stgd645ee2b-9dfe-42fc-adb2-896947de0291/dqc_reference
[2024-01-24 14:20:00,981] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:00,986] [INFO] Task started: Prodigal
[2024-01-24 14:20:00,986] [INFO] Running command: gunzip -c /var/lib/cwl/stgf81da26b-ccb6-420d-8566-78916a67acc5/GCF_006351005.1_ASM635100v1_genomic.fna.gz | prodigal -d GCF_006351005.1_ASM635100v1_genomic.fna/cds.fna -a GCF_006351005.1_ASM635100v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:09,914] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:09,914] [INFO] Task started: HMMsearch
[2024-01-24 14:20:09,915] [INFO] Running command: hmmsearch --tblout GCF_006351005.1_ASM635100v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd645ee2b-9dfe-42fc-adb2-896947de0291/dqc_reference/reference_markers.hmm GCF_006351005.1_ASM635100v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:10,188] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:10,189] [INFO] Found 6/6 markers.
[2024-01-24 14:20:10,227] [INFO] Query marker FASTA was written to GCF_006351005.1_ASM635100v1_genomic.fna/markers.fasta
[2024-01-24 14:20:10,228] [INFO] Task started: Blastn
[2024-01-24 14:20:10,228] [INFO] Running command: blastn -query GCF_006351005.1_ASM635100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd645ee2b-9dfe-42fc-adb2-896947de0291/dqc_reference/reference_markers.fasta -out GCF_006351005.1_ASM635100v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:11,450] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:11,454] [INFO] Selected 27 target genomes.
[2024-01-24 14:20:11,455] [INFO] Target genome list was writen to GCF_006351005.1_ASM635100v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:11,463] [INFO] Task started: fastANI
[2024-01-24 14:20:11,463] [INFO] Running command: fastANI --query /var/lib/cwl/stgf81da26b-ccb6-420d-8566-78916a67acc5/GCF_006351005.1_ASM635100v1_genomic.fna.gz --refList GCF_006351005.1_ASM635100v1_genomic.fna/target_genomes.txt --output GCF_006351005.1_ASM635100v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:34,348] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:34,349] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd645ee2b-9dfe-42fc-adb2-896947de0291/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:34,349] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd645ee2b-9dfe-42fc-adb2-896947de0291/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:34,377] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:20:34,377] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:20:34,377] [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
Beutenbergia cavernae	strain=DSM 12333	GCA_000023105.1	84757	84757	type	True	78.4267	520	1060	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.359	474	1060	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	78.251	476	1060	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	78.241	439	1060	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	78.2067	479	1060	95	below_threshold
Pseudactinotalea terrae	strain=KACC 16542	GCA_009733845.1	1743262	1743262	type	True	78.1376	394	1060	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	78.0889	437	1060	95	below_threshold
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	78.0849	496	1060	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	78.0722	417	1060	95	below_threshold
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	78.0684	444	1060	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	77.9854	492	1060	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	77.9623	501	1060	95	below_threshold
Cellulomonas shaoxiangyii	strain=Z28	GCA_004798685.1	2566013	2566013	type	True	77.9554	483	1060	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.9315	496	1060	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	77.7946	454	1060	95	below_threshold
Ruania suaedae	strain=LR1S40	GCA_021049265.1	2897774	2897774	type	True	77.7753	320	1060	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	77.7347	380	1060	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	77.7275	411	1060	95	below_threshold
Oerskovia enterophila	strain=DSM 43852	GCA_001692445.1	43678	43678	type	True	77.6483	408	1060	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	77.645	445	1060	95	below_threshold
Occultella aeris	strain=CIP 111667	GCA_902703175.1	2761496	2761496	type	True	77.5145	415	1060	95	below_threshold
Promicromonospora citrea	strain=JCM 3051	GCA_014647735.1	43677	43677	type	True	77.4583	475	1060	95	below_threshold
Brachybacterium halotolerans	strain=MASK1Z-5	GCA_016623465.1	2795215	2795215	type	True	76.8221	286	1060	95	below_threshold
Brachybacterium halotolerans subsp. kimchii	strain=CBA3105	GCA_020792675.1	2887346	2795215	type	True	76.7962	288	1060	95	below_threshold
Streptomyces daqingensis	strain=CGMCC 4.7178	GCA_014645895.1	1472640	1472640	type	True	76.1595	237	1060	95	below_threshold
Actinacidiphila yanglinensis	strain=CGMCC 4.2023	GCA_900107965.1	310779	310779	type	True	76.0202	352	1060	95	below_threshold
Streptomyces armeniacus	strain=ATCC 15676	GCA_003355155.1	83291	83291	type	True	75.8923	334	1060	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:34,379] [INFO] DFAST Taxonomy check result was written to GCF_006351005.1_ASM635100v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:34,380] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:34,380] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:34,380] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd645ee2b-9dfe-42fc-adb2-896947de0291/dqc_reference/checkm_data
[2024-01-24 14:20:34,381] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:34,423] [INFO] Task started: CheckM
[2024-01-24 14:20:34,423] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006351005.1_ASM635100v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006351005.1_ASM635100v1_genomic.fna/checkm_input GCF_006351005.1_ASM635100v1_genomic.fna/checkm_result
[2024-01-24 14:21:19,565] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:19,567] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:19,587] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:19,587] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:19,588] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006351005.1_ASM635100v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:19,588] [INFO] Task started: Blastn
[2024-01-24 14:21:19,588] [INFO] Running command: blastn -query GCF_006351005.1_ASM635100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd645ee2b-9dfe-42fc-adb2-896947de0291/dqc_reference/reference_markers_gtdb.fasta -out GCF_006351005.1_ASM635100v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:21,393] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:21,397] [INFO] Selected 13 target genomes.
[2024-01-24 14:21:21,398] [INFO] Target genome list was writen to GCF_006351005.1_ASM635100v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:21,436] [INFO] Task started: fastANI
[2024-01-24 14:21:21,437] [INFO] Running command: fastANI --query /var/lib/cwl/stgf81da26b-ccb6-420d-8566-78916a67acc5/GCF_006351005.1_ASM635100v1_genomic.fna.gz --refList GCF_006351005.1_ASM635100v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006351005.1_ASM635100v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:32,097] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:32,120] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:32,121] [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_006351005.1	s__Miniimonas arenae	100.0	1054	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Miniimonas	95.0	98.18	97.40	0.91	0.83	3	conclusive
GCF_004786095.1	s__Serinibacter_A arcticus	80.7059	580	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Serinibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121705.1	s__Serinibacter_A sp003121705	80.7014	633	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Serinibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751805.1	s__Salana multivorans	80.5379	617	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Salana	95.0	99.05	99.05	0.93	0.93	2	-
GCF_002563925.1	s__Serinibacter salmoneus	79.2274	435	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Serinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733795.1	s__Pseudactinotalea caeni	78.5947	483	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Pseudactinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708885.1	s__Cellulomonas sp000708885	78.2799	413	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409475.1	s__Cellulomonas hominis_B	78.1463	460	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552375.1	s__Cellulomonas iranensis	78.1129	492	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.21	97.89	0.91	0.88	6	-
GCF_002797595.1	s__Sediminihabitans luteus	78.0766	444	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sediminihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001692445.1	s__Oerskovia enterophila	77.6867	403	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	98.35	97.89	0.90	0.89	4	-
GCA_012514545.1	s__Actinotalea sp012514545	77.2939	359	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645895.1	s__Streptomyces daqingensis	76.1534	238	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.38	0.92	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:32,123] [INFO] GTDB search result was written to GCF_006351005.1_ASM635100v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:32,123] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:32,131] [INFO] DFAST_QC result json was written to GCF_006351005.1_ASM635100v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:32,131] [INFO] DFAST_QC completed!
[2024-01-24 14:21:32,132] [INFO] Total running time: 0h1m32s