[2024-01-25 19:01:35,805] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:01:35,807] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:01:35,807] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1104cc7-149f-4020-99ff-6e39e9eb4f37/dqc_reference
[2024-01-25 19:01:37,057] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:01:37,057] [INFO] Task started: Prodigal
[2024-01-25 19:01:37,058] [INFO] Running command: gunzip -c /var/lib/cwl/stg42ea7408-644e-4fd3-8a17-191d94d5acbf/GCF_000231035.2_ASM23103v3_genomic.fna.gz | prodigal -d GCF_000231035.2_ASM23103v3_genomic.fna/cds.fna -a GCF_000231035.2_ASM23103v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:01:48,982] [INFO] Task succeeded: Prodigal
[2024-01-25 19:01:48,982] [INFO] Task started: HMMsearch
[2024-01-25 19:01:48,983] [INFO] Running command: hmmsearch --tblout GCF_000231035.2_ASM23103v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1104cc7-149f-4020-99ff-6e39e9eb4f37/dqc_reference/reference_markers.hmm GCF_000231035.2_ASM23103v3_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:01:49,236] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:01:49,237] [INFO] Found 6/6 markers.
[2024-01-25 19:01:49,274] [INFO] Query marker FASTA was written to GCF_000231035.2_ASM23103v3_genomic.fna/markers.fasta
[2024-01-25 19:01:49,274] [INFO] Task started: Blastn
[2024-01-25 19:01:49,274] [INFO] Running command: blastn -query GCF_000231035.2_ASM23103v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1104cc7-149f-4020-99ff-6e39e9eb4f37/dqc_reference/reference_markers.fasta -out GCF_000231035.2_ASM23103v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:50,494] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:50,496] [INFO] Selected 16 target genomes.
[2024-01-25 19:01:50,497] [INFO] Target genome list was writen to GCF_000231035.2_ASM23103v3_genomic.fna/target_genomes.txt
[2024-01-25 19:01:50,502] [INFO] Task started: fastANI
[2024-01-25 19:01:50,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg42ea7408-644e-4fd3-8a17-191d94d5acbf/GCF_000231035.2_ASM23103v3_genomic.fna.gz --refList GCF_000231035.2_ASM23103v3_genomic.fna/target_genomes.txt --output GCF_000231035.2_ASM23103v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:11,050] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:11,051] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1104cc7-149f-4020-99ff-6e39e9eb4f37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:11,051] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1104cc7-149f-4020-99ff-6e39e9eb4f37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:11,062] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:02:11,062] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:02:11,063] [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
Saccharomonospora iraqiensis subsp. paurometabolica	strain=YIM 90007	GCA_000231035.3	208085	52698	type	True	99.9999	1511	1517	95	conclusive
Saccharomonospora iraqiensis	strain=IQ-H1	GCA_000430445.1	52698	52698	type	True	95.9076	1076	1517	95	conclusive
Saccharomonospora halophila	strain=8	GCA_000383775.1	129922	129922	type	True	93.3862	1004	1517	95	below_threshold
Saccharomonospora saliphila	strain=YIM 90502	GCA_000383795.1	369829	369829	type	True	83.0408	873	1517	95	below_threshold
Saccharomonospora piscinae	strain=KCTC 19743	GCA_005862235.1	687388	687388	type	True	80.6292	817	1517	95	below_threshold
Saccharomonospora azurea	strain=NA-128	GCA_000231055.3	40988	40988	type	True	80.3879	803	1517	95	below_threshold
Saccharomonospora cyanea	strain=NA-134	GCA_000244975.1	40989	40989	type	True	80.295	823	1517	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.7312	803	1517	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	79.6821	811	1517	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	79.6512	810	1517	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	79.3036	763	1517	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.211	766	1517	95	below_threshold
Amycolatopsis alkalitolerans	strain=SYSUP0005	GCA_006152065.1	2547244	2547244	type	True	78.6776	640	1517	95	below_threshold
Haloechinothrix aidingensis	strain=YIM 98757	GCA_013450155.1	2752311	2752311	type	True	78.3109	487	1517	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.1129	788	1517	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	77.8254	609	1517	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:02:11,064] [INFO] DFAST Taxonomy check result was written to GCF_000231035.2_ASM23103v3_genomic.fna/tc_result.tsv
[2024-01-25 19:02:11,064] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:11,065] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:11,065] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1104cc7-149f-4020-99ff-6e39e9eb4f37/dqc_reference/checkm_data
[2024-01-25 19:02:11,066] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:11,113] [INFO] Task started: CheckM
[2024-01-25 19:02:11,113] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000231035.2_ASM23103v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000231035.2_ASM23103v3_genomic.fna/checkm_input GCF_000231035.2_ASM23103v3_genomic.fna/checkm_result
[2024-01-25 19:02:43,520] [INFO] Task succeeded: CheckM
[2024-01-25 19:02:43,521] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:02:43,543] [INFO] ===== Completeness check finished =====
[2024-01-25 19:02:43,543] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:02:43,543] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000231035.2_ASM23103v3_genomic.fna/markers.fasta)
[2024-01-25 19:02:43,543] [INFO] Task started: Blastn
[2024-01-25 19:02:43,543] [INFO] Running command: blastn -query GCF_000231035.2_ASM23103v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1104cc7-149f-4020-99ff-6e39e9eb4f37/dqc_reference/reference_markers_gtdb.fasta -out GCF_000231035.2_ASM23103v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:45,394] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:45,397] [INFO] Selected 11 target genomes.
[2024-01-25 19:02:45,397] [INFO] Target genome list was writen to GCF_000231035.2_ASM23103v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:02:45,404] [INFO] Task started: fastANI
[2024-01-25 19:02:45,404] [INFO] Running command: fastANI --query /var/lib/cwl/stg42ea7408-644e-4fd3-8a17-191d94d5acbf/GCF_000231035.2_ASM23103v3_genomic.fna.gz --refList GCF_000231035.2_ASM23103v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000231035.2_ASM23103v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:02:58,638] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:58,646] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:02:58,646] [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_000231035.2	s__Saccharomonospora paurometabolica	99.9999	1511	1517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	96.0038	N/A	N/A	N/A	N/A	1	conclusive
GCF_000430445.1	s__Saccharomonospora iraqiensis	95.888	1076	1517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	96.0038	N/A	N/A	N/A	N/A	1	-
GCF_000383775.1	s__Saccharomonospora halophila	93.3862	1004	1517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383795.1	s__Saccharomonospora saliphila	83.0551	871	1517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005862235.1	s__Saccharomonospora piscinae	80.6121	819	1517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	98.79	98.27	0.95	0.94	3	-
GCF_000244975.1	s__Saccharomonospora cyanea	80.2254	834	1517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464705.1	s__Saccharomonospora sp016464705	79.9042	835	1517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005146945.1	s__Saccharomonospora endophytica	79.7212	845	1517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.14	99.02	0.90	0.90	3	-
GCF_900115565.1	s__Yuhushiella arida	79.6077	818	1517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_006152065.1	s__Amycolatopsis alkalitolerans	78.6505	644	1517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013450155.1	s__Haloechinothrix aidingensis	78.2981	491	1517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Haloechinothrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:02:58,648] [INFO] GTDB search result was written to GCF_000231035.2_ASM23103v3_genomic.fna/result_gtdb.tsv
[2024-01-25 19:02:58,648] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:02:58,651] [INFO] DFAST_QC result json was written to GCF_000231035.2_ASM23103v3_genomic.fna/dqc_result.json
[2024-01-25 19:02:58,651] [INFO] DFAST_QC completed!
[2024-01-25 19:02:58,651] [INFO] Total running time: 0h1m23s