[2024-01-24 13:36:44,366] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:44,368] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:44,368] [INFO] DQC Reference Directory: /var/lib/cwl/stg39c229d3-290f-4b10-bf2a-acd217092f05/dqc_reference
[2024-01-24 13:36:45,676] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:45,677] [INFO] Task started: Prodigal
[2024-01-24 13:36:45,677] [INFO] Running command: gunzip -c /var/lib/cwl/stg36b5adc7-ecef-46a0-904e-388a5bb8a3a4/GCF_014649855.1_ASM1464985v1_genomic.fna.gz | prodigal -d GCF_014649855.1_ASM1464985v1_genomic.fna/cds.fna -a GCF_014649855.1_ASM1464985v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:06,150] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:06,150] [INFO] Task started: HMMsearch
[2024-01-24 13:37:06,151] [INFO] Running command: hmmsearch --tblout GCF_014649855.1_ASM1464985v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39c229d3-290f-4b10-bf2a-acd217092f05/dqc_reference/reference_markers.hmm GCF_014649855.1_ASM1464985v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:06,457] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:06,458] [INFO] Found 6/6 markers.
[2024-01-24 13:37:06,514] [INFO] Query marker FASTA was written to GCF_014649855.1_ASM1464985v1_genomic.fna/markers.fasta
[2024-01-24 13:37:06,514] [INFO] Task started: Blastn
[2024-01-24 13:37:06,515] [INFO] Running command: blastn -query GCF_014649855.1_ASM1464985v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39c229d3-290f-4b10-bf2a-acd217092f05/dqc_reference/reference_markers.fasta -out GCF_014649855.1_ASM1464985v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:08,060] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:08,064] [INFO] Selected 20 target genomes.
[2024-01-24 13:37:08,064] [INFO] Target genome list was writen to GCF_014649855.1_ASM1464985v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:08,079] [INFO] Task started: fastANI
[2024-01-24 13:37:08,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg36b5adc7-ecef-46a0-904e-388a5bb8a3a4/GCF_014649855.1_ASM1464985v1_genomic.fna.gz --refList GCF_014649855.1_ASM1464985v1_genomic.fna/target_genomes.txt --output GCF_014649855.1_ASM1464985v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:49,194] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:49,195] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39c229d3-290f-4b10-bf2a-acd217092f05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:49,195] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39c229d3-290f-4b10-bf2a-acd217092f05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:49,212] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:49,212] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:49,212] [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
Streptomyces roseolus	strain=JCM 4411	GCA_014649855.1	67358	67358	type	True	100.0	2641	2642	95	conclusive
Streptomyces hydrogenans	strain=NBRC 13475	GCA_020521255.1	1873719	1873719	type	True	91.3248	2034	2642	95	below_threshold
Streptomyces hydrogenans	strain=JCM 4771	GCA_014656075.1	1873719	1873719	type	True	91.1788	1983	2642	95	below_threshold
Streptomyces filamentosus	strain=JCM 4122	GCA_014654895.1	67294	67294	type	True	90.881	2004	2642	95	below_threshold
Streptomyces omiyaensis	strain=JCM 4806	GCA_014650895.1	68247	68247	type	True	90.7376	2002	2642	95	below_threshold
Streptomyces termitum	strain=JCM 4518	GCA_014650175.1	67368	67368	type	True	89.3675	1753	2642	95	below_threshold
Streptomyces cinereoruber	strain=JCM 4205	GCA_014649095.1	67260	67260	type	True	87.1316	1667	2642	95	below_threshold
Streptomyces cinereoruber	strain=NRRL ISP-5012	GCA_014197485.1	67260	67260	type	True	87.0956	1704	2642	95	below_threshold
Streptomyces cinereoruber	strain=ATCC 19740	GCA_009299385.1	67260	67260	type	True	87.0901	1706	2642	95	below_threshold
Streptomyces cinereoruber	strain=JCM4205	GCA_019880525.1	67260	67260	type	True	87.0438	1703	2642	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	86.913	1786	2642	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_021432215.1	54571	54571	type	True	86.8254	1409	2642	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	82.9736	1116	2642	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.7681	1394	2642	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	82.7465	1162	2642	95	below_threshold
Pedococcus dokdonensis	strain=DSM 22329	GCA_900104525.1	443156	443156	type	True	76.7931	430	2642	95	below_threshold
Microbacterium paraoxydans	strain=NBRC 103076	GCA_001552495.1	199592	199592	suspected-type	True	76.1667	276	2642	95	below_threshold
Microbacterium paraoxydans	strain=DSM 15019	GCA_900105335.1	199592	199592	suspected-type	True	76.1352	297	2642	95	below_threshold
Rhodococcus jostii	strain=DSM 44719	GCA_900105375.1	132919	132919	type	True	75.7736	451	2642	95	below_threshold
Rhodococcus wratislaviensis	strain=NCTC13229	GCA_900455735.1	44752	44752	suspected-type	True	75.7463	423	2642	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:49,214] [INFO] DFAST Taxonomy check result was written to GCF_014649855.1_ASM1464985v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:49,215] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:49,215] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:49,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39c229d3-290f-4b10-bf2a-acd217092f05/dqc_reference/checkm_data
[2024-01-24 13:37:49,216] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:49,292] [INFO] Task started: CheckM
[2024-01-24 13:37:49,293] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649855.1_ASM1464985v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649855.1_ASM1464985v1_genomic.fna/checkm_input GCF_014649855.1_ASM1464985v1_genomic.fna/checkm_result
[2024-01-24 13:39:26,876] [INFO] Task succeeded: CheckM
[2024-01-24 13:39:26,878] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:39:26,900] [INFO] ===== Completeness check finished =====
[2024-01-24 13:39:26,901] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:39:26,901] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649855.1_ASM1464985v1_genomic.fna/markers.fasta)
[2024-01-24 13:39:26,901] [INFO] Task started: Blastn
[2024-01-24 13:39:26,901] [INFO] Running command: blastn -query GCF_014649855.1_ASM1464985v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39c229d3-290f-4b10-bf2a-acd217092f05/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649855.1_ASM1464985v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:39:29,580] [INFO] Task succeeded: Blastn
[2024-01-24 13:39:29,584] [INFO] Selected 16 target genomes.
[2024-01-24 13:39:29,584] [INFO] Target genome list was writen to GCF_014649855.1_ASM1464985v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:39:29,604] [INFO] Task started: fastANI
[2024-01-24 13:39:29,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg36b5adc7-ecef-46a0-904e-388a5bb8a3a4/GCF_014649855.1_ASM1464985v1_genomic.fna.gz --refList GCF_014649855.1_ASM1464985v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649855.1_ASM1464985v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:40:07,053] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:07,066] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:40:07,066] [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_014649855.1	s__Streptomyces roseolus	100.0	2641	2642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012927245.1	s__Streptomyces sp012927245	94.2561	2010	2642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000719555.1	s__Streptomyces sp000719555	91.4328	1907	2642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656075.1	s__Streptomyces hydrogenans	91.1936	1981	2642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	97.53	0.88	0.87	3	-
GCA_000721275.1	s__Streptomyces sp000721275	91.11	1937	2642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654895.1	s__Streptomyces filamentosus	90.9272	1998	2642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.28	96.27	0.93	0.92	4	-
GCF_014650895.1	s__Streptomyces omiyaensis	90.7261	2004	2642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650175.1	s__Streptomyces termitum	89.3303	1758	2642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105415.1	s__Streptomyces sp900105415	86.8774	1815	2642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.85	0.85	2	-
GCF_014649755.1	s__Streptomyces litmocidini	86.8567	1761	2642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.07	95.07	0.85	0.85	2	-
GCF_000716445.1	s__Streptomyces wedmorensis	86.5973	1826	2642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	97.63	0.94	0.88	3	-
GCA_002128465.1	s__Streptomyces pharetrae	82.0309	1332	2642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002911015.1	s__Streptomyces populi	81.6601	1375	2642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.82	0.82	2	-
GCF_013055795.1	s__Streptomyces sp013055795	80.8828	1162	2642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331005.1	s__Streptomyces turgidiscabies	80.6626	1228	2642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.67	0.92	0.88	3	-
GCF_003594885.1	s__Vallicoccus soli	76.4879	672	2642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Vallicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:40:07,068] [INFO] GTDB search result was written to GCF_014649855.1_ASM1464985v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:40:07,069] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:40:07,073] [INFO] DFAST_QC result json was written to GCF_014649855.1_ASM1464985v1_genomic.fna/dqc_result.json
[2024-01-24 13:40:07,073] [INFO] DFAST_QC completed!
[2024-01-24 13:40:07,073] [INFO] Total running time: 0h3m23s