[2023-06-29 14:37:45,553] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:37:45,556] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:37:45,556] [INFO] DQC Reference Directory: /var/lib/cwl/stga4c8529e-3062-4861-92d8-48ac8b00bd8e/dqc_reference
[2023-06-29 14:37:47,090] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:37:47,091] [INFO] Task started: Prodigal
[2023-06-29 14:37:47,091] [INFO] Running command: gunzip -c /var/lib/cwl/stgeaccce3a-0b9f-4deb-99cb-a6f594bb4662/GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:38:00,671] [INFO] Task succeeded: Prodigal
[2023-06-29 14:38:00,672] [INFO] Task started: HMMsearch
[2023-06-29 14:38:00,672] [INFO] Running command: hmmsearch --tblout GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4c8529e-3062-4861-92d8-48ac8b00bd8e/dqc_reference/reference_markers.hmm GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:38:00,960] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:38:00,962] [INFO] Found 6/6 markers.
[2023-06-29 14:38:01,006] [INFO] Query marker FASTA was written to GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 14:38:01,006] [INFO] Task started: Blastn
[2023-06-29 14:38:01,006] [INFO] Running command: blastn -query GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga4c8529e-3062-4861-92d8-48ac8b00bd8e/dqc_reference/reference_markers.fasta -out GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:38:01,641] [INFO] Task succeeded: Blastn
[2023-06-29 14:38:01,650] [INFO] Selected 17 target genomes.
[2023-06-29 14:38:01,650] [INFO] Target genome list was writen to GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 14:38:01,655] [INFO] Task started: fastANI
[2023-06-29 14:38:01,656] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaccce3a-0b9f-4deb-99cb-a6f594bb4662/GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:38:16,232] [INFO] Task succeeded: fastANI
[2023-06-29 14:38:16,233] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4c8529e-3062-4861-92d8-48ac8b00bd8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:38:16,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4c8529e-3062-4861-92d8-48ac8b00bd8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:38:16,241] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:38:16,241] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:38:16,241] [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 laurentii	strain=ATCC 31255	GCA_002355495.1	39478	39478	type	True	74.8607	53	1401	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	74.8365	50	1401	95	below_threshold
Actinacidiphila guanduensis	strain=CGMCC 4.2022	GCA_900103985.1	310781	310781	type	True	74.7594	58	1401	95	below_threshold
Saccharopolyspora antimicrobica	strain=DSM 45119	GCA_003635025.1	455193	455193	type	True	74.6738	64	1401	95	below_threshold
Saccharopolyspora kobensis	strain=ATCC 20501	GCA_900108315.1	146035	146035	type	True	74.6697	61	1401	95	below_threshold
Saccharopolyspora hirsuta	strain=VKM Ac-666	GCA_008630535.1	1837	1837	type	True	74.6166	62	1401	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:38:16,243] [INFO] DFAST Taxonomy check result was written to GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 14:38:16,244] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:38:16,244] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:38:16,244] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4c8529e-3062-4861-92d8-48ac8b00bd8e/dqc_reference/checkm_data
[2023-06-29 14:38:16,246] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:38:16,295] [INFO] Task started: CheckM
[2023-06-29 14:38:16,295] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 14:39:00,925] [INFO] Task succeeded: CheckM
[2023-06-29 14:39:00,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:39:00,949] [INFO] ===== Completeness check finished =====
[2023-06-29 14:39:00,950] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:39:00,950] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 14:39:00,950] [INFO] Task started: Blastn
[2023-06-29 14:39:00,951] [INFO] Running command: blastn -query GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga4c8529e-3062-4861-92d8-48ac8b00bd8e/dqc_reference/reference_markers_gtdb.fasta -out GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:39:01,828] [INFO] Task succeeded: Blastn
[2023-06-29 14:39:01,834] [INFO] Selected 22 target genomes.
[2023-06-29 14:39:01,834] [INFO] Target genome list was writen to GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:39:01,850] [INFO] Task started: fastANI
[2023-06-29 14:39:01,851] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaccce3a-0b9f-4deb-99cb-a6f594bb4662/GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:39:14,559] [INFO] Task succeeded: fastANI
[2023-06-29 14:39:14,572] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:39:14,572] [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
GCA_002343445.1	s__UBA2387 sp002343445	99.9464	1094	1401	d__Bacteria;p__Armatimonadota;c__Fimbriimonadia;o__Fimbriimonadales;f__Fimbriimonadaceae;g__UBA2387	95.0	99.91	99.91	0.95	0.95	2	conclusive
GCA_016179045.1	s__JACOSL01 sp016179045	76.2637	73	1401	d__Bacteria;p__Armatimonadota;c__Fimbriimonadia;o__Fimbriimonadales;f__Fimbriimonadaceae;g__JACOSL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898035.1	s__55-13 sp001898035	76.0212	52	1401	d__Bacteria;p__Armatimonadota;c__Fimbriimonadia;o__Fimbriimonadales;f__Fimbriimonadaceae;g__55-13	95.0	99.96	99.96	0.99	0.99	2	-
GCA_016223145.1	s__H1-ARM1 sp016223145	75.8996	109	1401	d__Bacteria;p__Armatimonadota;c__Fimbriimonadia;o__Fimbriimonadales;f__Fimbriimonadaceae;g__H1-ARM1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162095.1	s__UphvI-Ar2 sp002162095	75.7559	68	1401	d__Bacteria;p__Armatimonadota;c__Fimbriimonadia;o__Fimbriimonadales;f__Fimbriimonadaceae;g__UphvI-Ar2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002344135.1	s__UBA6659 sp002344135	75.7224	87	1401	d__Bacteria;p__Armatimonadota;c__Fimbriimonadia;o__Fimbriimonadales;f__Fimbriimonadaceae;g__UBA6659	95.0	99.97	99.93	0.97	0.95	8	-
GCA_002355495.1	s__Streptomyces laurentii	74.8607	53	1401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526095.1	s__WYBA01 sp011526095	74.7204	93	1401	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__WYBA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 14:39:14,574] [INFO] GTDB search result was written to GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 14:39:14,575] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:39:14,578] [INFO] DFAST_QC result json was written to GCA_937967415.1_SRR1506984_bin.122_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 14:39:14,578] [INFO] DFAST_QC completed!
[2023-06-29 14:39:14,578] [INFO] Total running time: 0h1m29s