[2024-01-24 13:09:43,311] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:43,313] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:43,313] [INFO] DQC Reference Directory: /var/lib/cwl/stge229c4f2-8a00-4214-b638-633c4558531a/dqc_reference
[2024-01-24 13:09:44,540] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:44,541] [INFO] Task started: Prodigal
[2024-01-24 13:09:44,541] [INFO] Running command: gunzip -c /var/lib/cwl/stgafe4e6c8-2ff7-430d-ad41-81eee070b921/GCF_008704575.1_ASM870457v1_genomic.fna.gz | prodigal -d GCF_008704575.1_ASM870457v1_genomic.fna/cds.fna -a GCF_008704575.1_ASM870457v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:06,093] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:06,094] [INFO] Task started: HMMsearch
[2024-01-24 13:10:06,094] [INFO] Running command: hmmsearch --tblout GCF_008704575.1_ASM870457v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge229c4f2-8a00-4214-b638-633c4558531a/dqc_reference/reference_markers.hmm GCF_008704575.1_ASM870457v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:06,429] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:06,431] [INFO] Found 6/6 markers.
[2024-01-24 13:10:06,491] [INFO] Query marker FASTA was written to GCF_008704575.1_ASM870457v1_genomic.fna/markers.fasta
[2024-01-24 13:10:06,491] [INFO] Task started: Blastn
[2024-01-24 13:10:06,491] [INFO] Running command: blastn -query GCF_008704575.1_ASM870457v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge229c4f2-8a00-4214-b638-633c4558531a/dqc_reference/reference_markers.fasta -out GCF_008704575.1_ASM870457v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:07,961] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:07,967] [INFO] Selected 19 target genomes.
[2024-01-24 13:10:07,967] [INFO] Target genome list was writen to GCF_008704575.1_ASM870457v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:08,005] [INFO] Task started: fastANI
[2024-01-24 13:10:08,006] [INFO] Running command: fastANI --query /var/lib/cwl/stgafe4e6c8-2ff7-430d-ad41-81eee070b921/GCF_008704575.1_ASM870457v1_genomic.fna.gz --refList GCF_008704575.1_ASM870457v1_genomic.fna/target_genomes.txt --output GCF_008704575.1_ASM870457v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:51,256] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:51,256] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge229c4f2-8a00-4214-b638-633c4558531a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:51,257] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge229c4f2-8a00-4214-b638-633c4558531a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:51,277] [INFO] Found 19 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:10:51,277] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:10:51,277] [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 galilaeus	strain=ATCC 14969	GCA_008704575.1	33899	33899	type	True	100.0	2584	2585	95	inconclusive
Streptomyces galilaeus	strain=JCM 4757	GCA_014650835.1	33899	33899	type	True	99.981	2524	2585	95	inconclusive
Streptomyces bobili	strain=NRRL B-1338	GCA_002154575.1	67280	67280	type	True	97.6287	1860	2585	95	inconclusive
Streptomyces phaeofaciens	strain=JCM 4125	GCA_014648915.1	68254	68254	type	True	87.0474	1993	2585	95	below_threshold
Streptomyces asoensis	strain=NBRC 13813	GCA_016860545.1	249586	249586	type	True	86.5978	1919	2585	95	below_threshold
Streptomyces humidus	strain=JCM 4386	GCA_014649655.1	52259	52259	type	True	86.1638	1813	2585	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	85.35	1804	2585	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	85.3342	1913	2585	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	85.1331	1732	2585	95	below_threshold
Streptomyces chartreusis	strain=ATCC 14922	GCA_008704715.1	1969	1969	suspected-type	True	85.1303	1896	2585	95	below_threshold
Streptomyces pseudovenezuelae	strain=DSM 40212	GCA_001513955.1	67350	67350	type	True	85.1265	1861	2585	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	85.0551	1458	2585	95	below_threshold
Streptomyces canus	strain=DSM 40017	GCA_001514145.1	58343	58343	suspected-type	True	84.9838	1911	2585	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	84.9251	1658	2585	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.9207	1642	2585	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	84.6496	1695	2585	95	below_threshold
Streptomyces hyaluromycini	strain=NBRC 110483	GCA_002217755.1	1377993	1377993	type	True	84.5966	1805	2585	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000383595.1	42235	42235	type	True	84.1992	1721	2585	95	below_threshold
Streptomyces stelliscabiei	strain=DSM 41803	GCA_014873495.1	146820	146820	type	True	84.1423	1785	2585	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:51,279] [INFO] DFAST Taxonomy check result was written to GCF_008704575.1_ASM870457v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:51,280] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:51,280] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:51,280] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge229c4f2-8a00-4214-b638-633c4558531a/dqc_reference/checkm_data
[2024-01-24 13:10:51,281] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:51,371] [INFO] Task started: CheckM
[2024-01-24 13:10:51,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008704575.1_ASM870457v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008704575.1_ASM870457v1_genomic.fna/checkm_input GCF_008704575.1_ASM870457v1_genomic.fna/checkm_result
[2024-01-24 13:12:24,027] [INFO] Task succeeded: CheckM
[2024-01-24 13:12:24,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 13:12:24,060] [INFO] ===== Completeness check finished =====
[2024-01-24 13:12:24,060] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:12:24,061] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008704575.1_ASM870457v1_genomic.fna/markers.fasta)
[2024-01-24 13:12:24,061] [INFO] Task started: Blastn
[2024-01-24 13:12:24,062] [INFO] Running command: blastn -query GCF_008704575.1_ASM870457v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge229c4f2-8a00-4214-b638-633c4558531a/dqc_reference/reference_markers_gtdb.fasta -out GCF_008704575.1_ASM870457v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:26,114] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:26,120] [INFO] Selected 21 target genomes.
[2024-01-24 13:12:26,120] [INFO] Target genome list was writen to GCF_008704575.1_ASM870457v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:12:26,137] [INFO] Task started: fastANI
[2024-01-24 13:12:26,137] [INFO] Running command: fastANI --query /var/lib/cwl/stgafe4e6c8-2ff7-430d-ad41-81eee070b921/GCF_008704575.1_ASM870457v1_genomic.fna.gz --refList GCF_008704575.1_ASM870457v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008704575.1_ASM870457v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:12,934] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:12,956] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:12,957] [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_002154575.1	s__Streptomyces bobili	97.6071	1863	2585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.61	97.61	0.88	0.85	3	conclusive
GCF_001896135.2	s__Streptomyces phaeoluteigriseus	93.6689	2135	2585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	88.228	2055	2585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129855.1	s__Streptomyces sp900129855	87.076	1930	2585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.68	99.68	0.97	0.97	2	-
GCF_014648915.1	s__Streptomyces phaeofaciens	87.0213	1997	2585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110755.1	s__Streptomyces sp900110755	86.8276	1883	2585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019855.1	s__Streptomyces antibioticus_B	86.7789	1867	2585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.20	96.76	0.94	0.90	5	-
GCF_001746365.1	s__Streptomyces sp001746365	86.4276	1854	2585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514285.1	s__Streptomyces sp001514285	86.2423	1844	2585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649655.1	s__Streptomyces humidus	86.1757	1810	2585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685355.1	s__Streptomyces lincolnensis	85.5572	1921	2585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.97	0.95	3	-
GCF_000720805.1	s__Streptomyces violaceoruber_B	85.5296	1820	2585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.8346	N/A	N/A	N/A	N/A	1	-
GCF_003143935.1	s__Streptomyces sp003143935	85.4631	1870	2585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721105.1	s__Streptomyces cellulosae_A	85.4232	1832	2585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.8346	N/A	N/A	N/A	N/A	1	-
GCF_001514305.1	s__Streptomyces dysideae	85.3443	1805	2585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513955.1	s__Streptomyces pseudovenezuelae	85.1555	1854	2585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042075.1	s__Streptomyces sp008042075	85.0906	1863	2585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002128465.1	s__Streptomyces pharetrae	85.0883	1593	2585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001746295.1	s__Streptomyces sp001746295	85.0057	1865	2585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873495.1	s__Streptomyces stelliscabiei	84.1698	1781	2585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.87	99.68	0.98	0.96	4	-
GCF_000383595.1	s__Streptomyces bottropensis	84.1252	1732	2585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.99	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:12,958] [INFO] GTDB search result was written to GCF_008704575.1_ASM870457v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:12,959] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:12,963] [INFO] DFAST_QC result json was written to GCF_008704575.1_ASM870457v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:12,963] [INFO] DFAST_QC completed!
[2024-01-24 13:13:12,963] [INFO] Total running time: 0h3m30s