[2024-01-25 17:53:21,107] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:53:21,108] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:53:21,108] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc2468c5-02f4-4843-815b-b918b68e6933/dqc_reference
[2024-01-25 17:53:22,217] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:53:22,217] [INFO] Task started: Prodigal
[2024-01-25 17:53:22,218] [INFO] Running command: gunzip -c /var/lib/cwl/stgb81b828e-d3b3-453e-8de2-ded70b29487a/GCF_025151045.1_ASM2515104v1_genomic.fna.gz | prodigal -d GCF_025151045.1_ASM2515104v1_genomic.fna/cds.fna -a GCF_025151045.1_ASM2515104v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:53:42,932] [INFO] Task succeeded: Prodigal
[2024-01-25 17:53:42,932] [INFO] Task started: HMMsearch
[2024-01-25 17:53:42,932] [INFO] Running command: hmmsearch --tblout GCF_025151045.1_ASM2515104v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc2468c5-02f4-4843-815b-b918b68e6933/dqc_reference/reference_markers.hmm GCF_025151045.1_ASM2515104v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:53:43,183] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:53:43,185] [INFO] Found 6/6 markers.
[2024-01-25 17:53:43,221] [INFO] Query marker FASTA was written to GCF_025151045.1_ASM2515104v1_genomic.fna/markers.fasta
[2024-01-25 17:53:43,222] [INFO] Task started: Blastn
[2024-01-25 17:53:43,222] [INFO] Running command: blastn -query GCF_025151045.1_ASM2515104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc2468c5-02f4-4843-815b-b918b68e6933/dqc_reference/reference_markers.fasta -out GCF_025151045.1_ASM2515104v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:43,778] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:43,781] [INFO] Selected 8 target genomes.
[2024-01-25 17:53:43,781] [INFO] Target genome list was writen to GCF_025151045.1_ASM2515104v1_genomic.fna/target_genomes.txt
[2024-01-25 17:53:43,794] [INFO] Task started: fastANI
[2024-01-25 17:53:43,794] [INFO] Running command: fastANI --query /var/lib/cwl/stgb81b828e-d3b3-453e-8de2-ded70b29487a/GCF_025151045.1_ASM2515104v1_genomic.fna.gz --refList GCF_025151045.1_ASM2515104v1_genomic.fna/target_genomes.txt --output GCF_025151045.1_ASM2515104v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:53:52,115] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:52,115] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc2468c5-02f4-4843-815b-b918b68e6933/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:53:52,116] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc2468c5-02f4-4843-815b-b918b68e6933/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:53:52,123] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:53:52,124] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:53:52,124] [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
Parabacteroides johnsonii	strain=DSM 18315	GCA_025151045.1	387661	387661	type	True	100.0	1580	1583	95	conclusive
Parabacteroides johnsonii	strain=DSM 18315	GCA_000156495.1	387661	387661	type	True	99.7966	1536	1583	95	conclusive
Parabacteroides merdae	strain=NCTC13052	GCA_900445495.1	46503	46503	type	True	91.0806	1109	1583	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	91.0768	1100	1583	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_000154105.1	46503	46503	type	True	91.0007	1088	1583	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	82.0822	119	1583	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	80.9623	116	1583	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:53:52,125] [INFO] DFAST Taxonomy check result was written to GCF_025151045.1_ASM2515104v1_genomic.fna/tc_result.tsv
[2024-01-25 17:53:52,127] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:53:52,127] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:53:52,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc2468c5-02f4-4843-815b-b918b68e6933/dqc_reference/checkm_data
[2024-01-25 17:53:52,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:53:52,174] [INFO] Task started: CheckM
[2024-01-25 17:53:52,175] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025151045.1_ASM2515104v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025151045.1_ASM2515104v1_genomic.fna/checkm_input GCF_025151045.1_ASM2515104v1_genomic.fna/checkm_result
[2024-01-25 17:54:49,995] [INFO] Task succeeded: CheckM
[2024-01-25 17:54:49,996] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:54:50,016] [INFO] ===== Completeness check finished =====
[2024-01-25 17:54:50,017] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:54:50,018] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025151045.1_ASM2515104v1_genomic.fna/markers.fasta)
[2024-01-25 17:54:50,018] [INFO] Task started: Blastn
[2024-01-25 17:54:50,018] [INFO] Running command: blastn -query GCF_025151045.1_ASM2515104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc2468c5-02f4-4843-815b-b918b68e6933/dqc_reference/reference_markers_gtdb.fasta -out GCF_025151045.1_ASM2515104v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:50,938] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:50,941] [INFO] Selected 8 target genomes.
[2024-01-25 17:54:50,941] [INFO] Target genome list was writen to GCF_025151045.1_ASM2515104v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:54:50,949] [INFO] Task started: fastANI
[2024-01-25 17:54:50,949] [INFO] Running command: fastANI --query /var/lib/cwl/stgb81b828e-d3b3-453e-8de2-ded70b29487a/GCF_025151045.1_ASM2515104v1_genomic.fna.gz --refList GCF_025151045.1_ASM2515104v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025151045.1_ASM2515104v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:54:59,841] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:59,847] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:54:59,847] [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_000156495.1	s__Parabacteroides johnsonii	99.7966	1536	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.42	96.67	0.88	0.77	13	conclusive
GCF_000154105.1	s__Parabacteroides merdae	91.0054	1087	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.97	97.44	0.89	0.77	85	-
GCF_014287585.1	s__Parabacteroides sp014287585	89.6251	1170	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.33	98.97	0.95	0.91	4	-
GCA_900760525.1	s__Parabacteroides sp900760525	88.1892	965	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.93	98.92	0.84	0.82	3	-
GCF_900155425.1	s__Parabacteroides massiliensis	88.0188	1003	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.33	99.33	0.93	0.93	2	-
GCA_910577325.1	s__Parabacteroides sp910577325	86.5455	837	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937385.1	s__Parabacteroides sp017937385	84.0149	781	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:54:59,849] [INFO] GTDB search result was written to GCF_025151045.1_ASM2515104v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:54:59,849] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:54:59,852] [INFO] DFAST_QC result json was written to GCF_025151045.1_ASM2515104v1_genomic.fna/dqc_result.json
[2024-01-25 17:54:59,852] [INFO] DFAST_QC completed!
[2024-01-25 17:54:59,852] [INFO] Total running time: 0h1m39s