[2024-01-25 19:34:21,009] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:34:21,021] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:34:21,021] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3d22b40-fdab-42bb-8450-4068ac40a152/dqc_reference
[2024-01-25 19:34:22,229] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:34:22,229] [INFO] Task started: Prodigal
[2024-01-25 19:34:22,230] [INFO] Running command: gunzip -c /var/lib/cwl/stg1255801e-26a6-4d33-97c7-6880ec127aa9/GCF_026153355.1_ASM2615335v1_genomic.fna.gz | prodigal -d GCF_026153355.1_ASM2615335v1_genomic.fna/cds.fna -a GCF_026153355.1_ASM2615335v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:34:39,007] [INFO] Task succeeded: Prodigal
[2024-01-25 19:34:39,008] [INFO] Task started: HMMsearch
[2024-01-25 19:34:39,008] [INFO] Running command: hmmsearch --tblout GCF_026153355.1_ASM2615335v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3d22b40-fdab-42bb-8450-4068ac40a152/dqc_reference/reference_markers.hmm GCF_026153355.1_ASM2615335v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:34:39,249] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:34:39,250] [INFO] Found 6/6 markers.
[2024-01-25 19:34:39,300] [INFO] Query marker FASTA was written to GCF_026153355.1_ASM2615335v1_genomic.fna/markers.fasta
[2024-01-25 19:34:39,300] [INFO] Task started: Blastn
[2024-01-25 19:34:39,300] [INFO] Running command: blastn -query GCF_026153355.1_ASM2615335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3d22b40-fdab-42bb-8450-4068ac40a152/dqc_reference/reference_markers.fasta -out GCF_026153355.1_ASM2615335v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:40,486] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:40,489] [INFO] Selected 20 target genomes.
[2024-01-25 19:34:40,489] [INFO] Target genome list was writen to GCF_026153355.1_ASM2615335v1_genomic.fna/target_genomes.txt
[2024-01-25 19:34:40,494] [INFO] Task started: fastANI
[2024-01-25 19:34:40,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg1255801e-26a6-4d33-97c7-6880ec127aa9/GCF_026153355.1_ASM2615335v1_genomic.fna.gz --refList GCF_026153355.1_ASM2615335v1_genomic.fna/target_genomes.txt --output GCF_026153355.1_ASM2615335v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:35:19,918] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:19,918] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3d22b40-fdab-42bb-8450-4068ac40a152/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:35:19,919] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3d22b40-fdab-42bb-8450-4068ac40a152/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:35:19,932] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:35:19,932] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:35:19,932] [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 lydicus	strain=ATCC 25470	GCA_004125245.1	47763	47763	suspected-type	True	88.8054	1869	2300	95	below_threshold
Streptomyces lydicus	strain=NRRL ISP-5461	GCA_000717345.1	47763	47763	suspected-type	True	88.7792	1869	2300	95	below_threshold
Streptomyces inhibens	strain=NEAU-D10	GCA_003389455.1	2293571	2293571	type	True	88.4076	1743	2300	95	below_threshold
Streptomyces angustmyceticus	strain=NRRL B-2347	GCA_002154415.1	285578	285578	type	True	88.136	1355	2300	95	below_threshold
Streptomyces angustmyceticus	strain=JCM 4053	GCA_019933235.1	285578	285578	type	True	88.1143	1792	2300	95	below_threshold
Streptomyces angustmyceticus	strain=NBRC 3934	GCA_009176265.1	285578	285578	type	True	88.0729	1766	2300	95	below_threshold
Streptomyces libani subsp. libani	strain=NBRC 13452	GCA_009811595.1	68044	68043	type	True	87.8913	1858	2300	95	below_threshold
Streptomyces lydicamycinicus	strain=NBRC 110027	GCA_000829715.2	1546107	1546107	type	True	87.8713	1812	2300	95	below_threshold
Streptomyces libani subsp. libani	strain=JCM 4322	GCA_014649275.1	68044	68043	type	True	87.8193	1834	2300	95	below_threshold
Streptomyces caniferus	strain=NBRC 15389	GCA_009811555.1	285557	285557	type	True	87.8186	1857	2300	95	below_threshold
Streptomyces sioyaensis	strain=DSM 40032	GCA_004122735.1	67364	67364	type	True	87.7782	1648	2300	95	below_threshold
Streptomyces glebosus	strain=NBRC 13786	GCA_009811575.1	249580	249580	type	True	87.7284	1825	2300	95	below_threshold
Streptomyces kronopolitis	strain=CGMCC 4.7323	GCA_014646275.1	1612435	1612435	type	True	87.7236	1682	2300	95	below_threshold
Streptomyces glebosus	strain=JCM 4954	GCA_014656235.1	249580	249580	type	True	87.6444	1789	2300	95	below_threshold
Streptomyces tubercidicus	strain=NBRC 13090	GCA_009811635.1	47759	47759	type	True	87.6383	1706	2300	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	85.4274	1541	2300	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	84.7061	1212	2300	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	84.0435	1580	2300	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	84.0238	1539	2300	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	83.9624	1578	2300	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:35:19,934] [INFO] DFAST Taxonomy check result was written to GCF_026153355.1_ASM2615335v1_genomic.fna/tc_result.tsv
[2024-01-25 19:35:19,934] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:35:19,935] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:35:19,935] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3d22b40-fdab-42bb-8450-4068ac40a152/dqc_reference/checkm_data
[2024-01-25 19:35:19,937] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:35:20,005] [INFO] Task started: CheckM
[2024-01-25 19:35:20,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026153355.1_ASM2615335v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026153355.1_ASM2615335v1_genomic.fna/checkm_input GCF_026153355.1_ASM2615335v1_genomic.fna/checkm_result
[2024-01-25 19:37:10,290] [INFO] Task succeeded: CheckM
[2024-01-25 19:37:10,291] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:37:10,319] [INFO] ===== Completeness check finished =====
[2024-01-25 19:37:10,319] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:37:10,320] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026153355.1_ASM2615335v1_genomic.fna/markers.fasta)
[2024-01-25 19:37:10,320] [INFO] Task started: Blastn
[2024-01-25 19:37:10,320] [INFO] Running command: blastn -query GCF_026153355.1_ASM2615335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3d22b40-fdab-42bb-8450-4068ac40a152/dqc_reference/reference_markers_gtdb.fasta -out GCF_026153355.1_ASM2615335v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:12,317] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:12,319] [INFO] Selected 12 target genomes.
[2024-01-25 19:37:12,320] [INFO] Target genome list was writen to GCF_026153355.1_ASM2615335v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:37:12,328] [INFO] Task started: fastANI
[2024-01-25 19:37:12,328] [INFO] Running command: fastANI --query /var/lib/cwl/stg1255801e-26a6-4d33-97c7-6880ec127aa9/GCF_026153355.1_ASM2615335v1_genomic.fna.gz --refList GCF_026153355.1_ASM2615335v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026153355.1_ASM2615335v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:37:38,527] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:38,535] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:37:38,536] [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_000720175.1	s__Streptomyces sp000720175	94.9821	2033	2300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.69	95.67	0.86	0.86	3	-
GCF_000717345.1	s__Streptomyces lydicus	88.7793	1869	2300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.39	95.38	0.95	0.89	6	-
GCF_003389455.1	s__Streptomyces inhibens	88.3934	1746	2300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176265.1	s__Streptomyces angustmyceticus	88.0438	1769	2300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	1.00	1.00	2	-
GCF_009811595.1	s__Streptomyces libani	87.8794	1858	2300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.04	96.45	0.91	0.86	12	-
GCF_009811555.1	s__Streptomyces caniferus	87.8126	1858	2300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270575.1	s__Streptomyces decoyicus	87.7944	1777	2300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.25	96.25	0.87	0.87	2	-
GCF_004122735.1	s__Streptomyces sioyaensis	87.7619	1650	2300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.26	95.36	0.89	0.84	9	-
GCF_014646275.1	s__Streptomyces kronopolitis	87.7139	1682	2300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811635.1	s__Streptomyces tubercidicus	87.6141	1707	2300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187385.1	s__Streptomyces sp900187385	87.5897	1803	2300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.51	0.98	0.96	9	-
GCF_001590865.1	s__Streptomyces sp001590865	87.1567	1579	2300	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 19:37:38,537] [INFO] GTDB search result was written to GCF_026153355.1_ASM2615335v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:37:38,538] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:37:38,541] [INFO] DFAST_QC result json was written to GCF_026153355.1_ASM2615335v1_genomic.fna/dqc_result.json
[2024-01-25 19:37:38,541] [INFO] DFAST_QC completed!
[2024-01-25 19:37:38,541] [INFO] Total running time: 0h3m18s