[2024-01-24 13:47:11,663] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:47:11,665] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:47:11,666] [INFO] DQC Reference Directory: /var/lib/cwl/stg18d96f5d-4ffd-461b-8e92-2fc7e9b69ab9/dqc_reference
[2024-01-24 13:47:13,081] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:47:13,082] [INFO] Task started: Prodigal
[2024-01-24 13:47:13,083] [INFO] Running command: gunzip -c /var/lib/cwl/stg50a26515-bbe5-442c-93a6-422329b037f6/GCF_014650915.1_ASM1465091v1_genomic.fna.gz | prodigal -d GCF_014650915.1_ASM1465091v1_genomic.fna/cds.fna -a GCF_014650915.1_ASM1465091v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:37,938] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:37,938] [INFO] Task started: HMMsearch
[2024-01-24 13:47:37,939] [INFO] Running command: hmmsearch --tblout GCF_014650915.1_ASM1465091v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18d96f5d-4ffd-461b-8e92-2fc7e9b69ab9/dqc_reference/reference_markers.hmm GCF_014650915.1_ASM1465091v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:38,302] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:38,304] [INFO] Found 6/6 markers.
[2024-01-24 13:47:38,372] [INFO] Query marker FASTA was written to GCF_014650915.1_ASM1465091v1_genomic.fna/markers.fasta
[2024-01-24 13:47:38,373] [INFO] Task started: Blastn
[2024-01-24 13:47:38,373] [INFO] Running command: blastn -query GCF_014650915.1_ASM1465091v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18d96f5d-4ffd-461b-8e92-2fc7e9b69ab9/dqc_reference/reference_markers.fasta -out GCF_014650915.1_ASM1465091v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:39,653] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:39,658] [INFO] Selected 26 target genomes.
[2024-01-24 13:47:39,658] [INFO] Target genome list was writen to GCF_014650915.1_ASM1465091v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:39,676] [INFO] Task started: fastANI
[2024-01-24 13:47:39,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg50a26515-bbe5-442c-93a6-422329b037f6/GCF_014650915.1_ASM1465091v1_genomic.fna.gz --refList GCF_014650915.1_ASM1465091v1_genomic.fna/target_genomes.txt --output GCF_014650915.1_ASM1465091v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:48:30,816] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:30,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18d96f5d-4ffd-461b-8e92-2fc7e9b69ab9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:48:30,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18d96f5d-4ffd-461b-8e92-2fc7e9b69ab9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:48:30,848] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:48:30,848] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:48:30,849] [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 poonensis	strain=JCM 4815	GCA_014650915.1	68255	68255	type	True	100.0	2837	2839	95	conclusive
Streptomyces ruber	strain=JCM 3131	GCA_014648075.1	83378	83378	type	True	89.3589	1837	2839	95	below_threshold
Streptomyces phyllanthi	strain=TISTR 2346	GCA_009377205.1	1803180	1803180	type	True	85.7276	1481	2839	95	below_threshold
Streptomyces spongiae	strain=NBRC 106415	GCA_009377185.1	565072	565072	type	True	85.4202	1489	2839	95	below_threshold
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	84.6377	1717	2839	95	below_threshold
Streptomyces avermitilis	strain=MA-4680	GCA_000009765.2	33903	33903	type	True	84.5856	1660	2839	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	84.5757	1634	2839	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	84.5243	1673	2839	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	84.4499	1655	2839	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	84.4207	1640	2839	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	84.4157	1698	2839	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	84.3344	1672	2839	95	below_threshold
Streptomyces capitiformicae	strain=CGMCC 4.7403	GCA_014653855.1	2014920	2014920	type	True	84.2923	1684	2839	95	below_threshold
Streptomyces capitiformicae	strain=1H-SSA4	GCA_002214185.1	2014920	2014920	type	True	84.2657	1689	2839	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.2626	1451	2839	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	84.2623	1659	2839	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	84.2583	1515	2839	95	below_threshold
Streptomyces calvus	strain=JCM 4326	GCA_014649315.1	67282	67282	type	True	84.2469	1656	2839	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	84.1324	1674	2839	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	84.0856	1634	2839	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	83.9825	1535	2839	95	below_threshold
Streptomyces naganishii	strain=JCM 4654	GCA_014650575.1	285447	285447	type	True	83.9691	1552	2839	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	83.8702	1710	2839	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	83.8326	1731	2839	95	below_threshold
Streptomyces longwoodensis	strain=DSM 41677	GCA_001514125.1	68231	68231	type	True	83.8251	1599	2839	95	below_threshold
Streptomyces thermoviolaceus subsp. thermoviolaceus	strain=NBRC 13905	GCA_012034235.1	66860	1952	type	True	83.1617	1273	2839	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:48:30,850] [INFO] DFAST Taxonomy check result was written to GCF_014650915.1_ASM1465091v1_genomic.fna/tc_result.tsv
[2024-01-24 13:48:30,851] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:48:30,851] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:48:30,851] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18d96f5d-4ffd-461b-8e92-2fc7e9b69ab9/dqc_reference/checkm_data
[2024-01-24 13:48:30,852] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:48:30,928] [INFO] Task started: CheckM
[2024-01-24 13:48:30,928] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650915.1_ASM1465091v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650915.1_ASM1465091v1_genomic.fna/checkm_input GCF_014650915.1_ASM1465091v1_genomic.fna/checkm_result
[2024-01-24 13:50:31,332] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:31,334] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:31,356] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:31,357] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:31,357] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650915.1_ASM1465091v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:31,357] [INFO] Task started: Blastn
[2024-01-24 13:50:31,358] [INFO] Running command: blastn -query GCF_014650915.1_ASM1465091v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18d96f5d-4ffd-461b-8e92-2fc7e9b69ab9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650915.1_ASM1465091v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:33,422] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:33,426] [INFO] Selected 19 target genomes.
[2024-01-24 13:50:33,426] [INFO] Target genome list was writen to GCF_014650915.1_ASM1465091v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:33,439] [INFO] Task started: fastANI
[2024-01-24 13:50:33,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg50a26515-bbe5-442c-93a6-422329b037f6/GCF_014650915.1_ASM1465091v1_genomic.fna.gz --refList GCF_014650915.1_ASM1465091v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650915.1_ASM1465091v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:13,855] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:13,873] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:13,873] [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_014650915.1	s__Streptomyces poonensis	100.0	2837	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000719105.1	s__Streptomyces sclerotialus_B	92.1083	1910	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648075.1	s__Streptomyces ruber	89.3345	1840	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009377205.1	s__Streptomyces phyllanthi	85.7179	1482	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650875.1	s__Streptomyces minutiscleroticus	84.6469	1715	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	98.56	0.90	0.90	2	-
GCF_009852415.1	s__Streptomyces sp009852415	84.4719	1713	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905725.1	s__Streptomyces sp001905725	84.4125	1681	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905845.1	s__Streptomyces sp001905845	84.3689	1686	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203535.1	s__Streptomyces griseostramineus	84.3566	1651	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.88	99.76	0.99	0.98	3	-
GCF_014905555.1	s__Streptomyces sp014905555	84.3368	1541	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006782915.1	s__Streptomyces calvus	84.2817	1654	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.66	99.31	0.97	0.96	5	-
GCF_001417775.1	s__Streptomyces sp001417775	84.177	1542	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001509795.1	s__Streptomyces sp001509795	84.1423	1514	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.33	98.67	0.96	0.93	3	-
GCF_000317595.1	s__Streptomyces ipomoeae	84.1285	1575	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.29	98.81	0.89	0.87	4	-
GCF_015160855.1	s__Streptomyces ferrugineus	84.1086	1679	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049285.1	s__Streptomyces sp019049285	83.8255	1658	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506575.1	s__Streptomyces mexicanus	83.8153	1498	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.95	96.19	0.87	0.78	3	-
GCF_014650035.1	s__Streptomyces lucensis	83.7792	1480	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507435.1	s__Streptomyces sp001507435	83.2733	1549	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.91	96.23	0.91	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:13,875] [INFO] GTDB search result was written to GCF_014650915.1_ASM1465091v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:13,875] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:13,880] [INFO] DFAST_QC result json was written to GCF_014650915.1_ASM1465091v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:13,880] [INFO] DFAST_QC completed!
[2024-01-24 13:51:13,880] [INFO] Total running time: 0h4m2s