[2024-01-25 19:47:50,679] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:50,680] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:50,681] [INFO] DQC Reference Directory: /var/lib/cwl/stg40f17d18-6974-4f89-861d-c2cec4e27ca7/dqc_reference
[2024-01-25 19:47:51,888] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:51,889] [INFO] Task started: Prodigal
[2024-01-25 19:47:51,889] [INFO] Running command: gunzip -c /var/lib/cwl/stg25253ebe-a12b-4001-a7b4-066461290f31/GCF_030803745.1_ASM3080374v1_genomic.fna.gz | prodigal -d GCF_030803745.1_ASM3080374v1_genomic.fna/cds.fna -a GCF_030803745.1_ASM3080374v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:48:47,331] [INFO] Task succeeded: Prodigal
[2024-01-25 19:48:47,331] [INFO] Task started: HMMsearch
[2024-01-25 19:48:47,331] [INFO] Running command: hmmsearch --tblout GCF_030803745.1_ASM3080374v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40f17d18-6974-4f89-861d-c2cec4e27ca7/dqc_reference/reference_markers.hmm GCF_030803745.1_ASM3080374v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:48:47,675] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:48:47,676] [INFO] Found 6/6 markers.
[2024-01-25 19:48:47,749] [INFO] Query marker FASTA was written to GCF_030803745.1_ASM3080374v1_genomic.fna/markers.fasta
[2024-01-25 19:48:47,750] [INFO] Task started: Blastn
[2024-01-25 19:48:47,750] [INFO] Running command: blastn -query GCF_030803745.1_ASM3080374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40f17d18-6974-4f89-861d-c2cec4e27ca7/dqc_reference/reference_markers.fasta -out GCF_030803745.1_ASM3080374v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:49,005] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:49,012] [INFO] Selected 18 target genomes.
[2024-01-25 19:48:49,012] [INFO] Target genome list was writen to GCF_030803745.1_ASM3080374v1_genomic.fna/target_genomes.txt
[2024-01-25 19:48:49,025] [INFO] Task started: fastANI
[2024-01-25 19:48:49,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg25253ebe-a12b-4001-a7b4-066461290f31/GCF_030803745.1_ASM3080374v1_genomic.fna.gz --refList GCF_030803745.1_ASM3080374v1_genomic.fna/target_genomes.txt --output GCF_030803745.1_ASM3080374v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:49:41,989] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:41,990] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40f17d18-6974-4f89-861d-c2cec4e27ca7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:49:41,990] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40f17d18-6974-4f89-861d-c2cec4e27ca7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:49:42,003] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:49:42,003] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:49:42,004] [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 hygroscopicus subsp. hygroscopicus	strain=NBRC 13472	GCA_001553455.1	68042	1912	type	True	97.8789	2576	3512	95	conclusive
Streptomyces sabulosicollis	strain=PRKS01-29	GCA_016103465.1	2715963	2715963	type	True	90.6704	1982	3512	95	below_threshold
Streptomyces antimycoticus	strain=NBRC 12839	GCA_005405925.1	68175	68175	type	True	90.4302	2437	3512	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	90.3819	2497	3512	95	below_threshold
Streptomyces iranensis	strain=DSM 41954	GCA_017874715.1	576784	576784	type	True	90.3708	2372	3512	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_003675955.1	1226757	1226757	type	True	90.3526	2515	3512	95	below_threshold
Streptomyces yatensis	strain=DSM 41771	GCA_018069625.1	155177	155177	type	True	90.3232	2390	3512	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_000418455.1	1226757	1226757	type	True	90.3228	2525	3512	95	below_threshold
Streptomyces javensis	strain=DSM 41764	GCA_016103505.1	114698	114698	type	True	89.9972	1878	3512	95	below_threshold
Streptomyces sparsogenes	strain=ATCC 25498	GCA_001704635.1	67365	67365	type	True	84.7794	1835	3512	95	below_threshold
Streptomyces pactum	strain=ATCC 27456	GCA_016031615.1	68249	68249	type	True	81.8309	1525	3512	95	below_threshold
Streptomyces olivoverticillatus	strain=CECT 3266	GCA_014203555.1	66427	66427	type	True	81.8226	1194	3512	95	below_threshold
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	81.3791	1348	3512	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	81.3699	1355	3512	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	81.1472	1414	3512	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	80.4803	1337	3512	95	below_threshold
Streptomyces fumanus	strain=JCM 4477	GCA_014655295.1	67302	67302	type	True	80.4451	1468	3512	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	80.1649	1362	3512	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:49:42,005] [INFO] DFAST Taxonomy check result was written to GCF_030803745.1_ASM3080374v1_genomic.fna/tc_result.tsv
[2024-01-25 19:49:42,009] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:49:42,009] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:49:42,009] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40f17d18-6974-4f89-861d-c2cec4e27ca7/dqc_reference/checkm_data
[2024-01-25 19:49:42,010] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:49:42,113] [INFO] Task started: CheckM
[2024-01-25 19:49:42,113] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030803745.1_ASM3080374v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030803745.1_ASM3080374v1_genomic.fna/checkm_input GCF_030803745.1_ASM3080374v1_genomic.fna/checkm_result
[2024-01-25 19:54:33,011] [INFO] Task succeeded: CheckM
[2024-01-25 19:54:33,012] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:54:33,037] [INFO] ===== Completeness check finished =====
[2024-01-25 19:54:33,038] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:54:33,039] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030803745.1_ASM3080374v1_genomic.fna/markers.fasta)
[2024-01-25 19:54:33,039] [INFO] Task started: Blastn
[2024-01-25 19:54:33,039] [INFO] Running command: blastn -query GCF_030803745.1_ASM3080374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40f17d18-6974-4f89-861d-c2cec4e27ca7/dqc_reference/reference_markers_gtdb.fasta -out GCF_030803745.1_ASM3080374v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:35,111] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:35,114] [INFO] Selected 16 target genomes.
[2024-01-25 19:54:35,114] [INFO] Target genome list was writen to GCF_030803745.1_ASM3080374v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:54:35,138] [INFO] Task started: fastANI
[2024-01-25 19:54:35,138] [INFO] Running command: fastANI --query /var/lib/cwl/stg25253ebe-a12b-4001-a7b4-066461290f31/GCF_030803745.1_ASM3080374v1_genomic.fna.gz --refList GCF_030803745.1_ASM3080374v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030803745.1_ASM3080374v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:55:27,914] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:27,924] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:55:27,925] [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_001553455.1	s__Streptomyces hygroscopicus	97.8879	2575	3512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.24	98.00	0.92	0.90	7	conclusive
GCA_005405945.1	s__Streptomyces violaceusniger	90.6171	2476	3512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.67	97.67	0.85	0.85	2	-
GCF_000147815.2	s__Streptomyces violaceusniger_A	90.4077	2408	3512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3301	95.69	95.54	0.80	0.80	4	-
GCF_005405925.1	s__Streptomyces antimycoticus	90.4008	2442	3512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.0185	97.28	96.80	0.85	0.81	7	-
GCF_017874715.1	s__Streptomyces iranensis	90.3939	2370	3512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.67	99.98	99.98	1.00	1.00	2	-
GCF_003675955.1	s__Streptomyces rapamycinicus	90.385	2509	3512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.67	99.95	99.91	0.99	0.99	3	-
GCF_018069625.1	s__Streptomyces yatensis	90.3451	2386	3512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.0185	N/A	N/A	N/A	N/A	1	-
GCF_018138715.1	s__Streptomyces asiaticus	90.335	2472	3512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	95.36	0.90	0.81	10	-
GCF_015689475.1	s__Streptomyces solisilvae	90.333	2450	3512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.71	97.94	0.94	0.86	10	-
GCF_016741935.1	s__Streptomyces sp016741935	90.1935	2473	3512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0488	N/A	N/A	N/A	N/A	1	-
GCF_000968685.2	s__Streptomyces antioxidans	89.9282	2094	3512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001704635.1	s__Streptomyces sparsogenes	84.7755	1835	3512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.81	0.87	0.87	2	-
GCF_014655595.1	s__Streptomyces griseocarneus	81.3328	1364	3512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649115.1	s__Streptomyces eurythermus	80.3043	1496	3512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	97.90	96.79	0.90	0.85	4	-
GCF_001278075.1	s__Streptomyces pristinaespiralis	80.2466	1348	3512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.86	99.72	0.99	0.98	3	-
GCF_001896135.2	s__Streptomyces phaeoluteigriseus	80.0058	1364	3512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:55:27,932] [INFO] GTDB search result was written to GCF_030803745.1_ASM3080374v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:55:27,933] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:55:27,940] [INFO] DFAST_QC result json was written to GCF_030803745.1_ASM3080374v1_genomic.fna/dqc_result.json
[2024-01-25 19:55:27,940] [INFO] DFAST_QC completed!
[2024-01-25 19:55:27,940] [INFO] Total running time: 0h7m37s