[2024-01-24 13:28:28,955] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:28,957] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:28,957] [INFO] DQC Reference Directory: /var/lib/cwl/stg13055dfd-503e-49ee-b100-1af9d5049f2e/dqc_reference
[2024-01-24 13:28:30,202] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:30,203] [INFO] Task started: Prodigal
[2024-01-24 13:28:30,203] [INFO] Running command: gunzip -c /var/lib/cwl/stg40e766f4-677a-41a6-b4b4-363c1bc45b3c/GCF_000374585.1_ASM37458v1_genomic.fna.gz | prodigal -d GCF_000374585.1_ASM37458v1_genomic.fna/cds.fna -a GCF_000374585.1_ASM37458v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:48,922] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:48,922] [INFO] Task started: HMMsearch
[2024-01-24 13:28:48,923] [INFO] Running command: hmmsearch --tblout GCF_000374585.1_ASM37458v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13055dfd-503e-49ee-b100-1af9d5049f2e/dqc_reference/reference_markers.hmm GCF_000374585.1_ASM37458v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:49,208] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:49,209] [INFO] Found 6/6 markers.
[2024-01-24 13:28:49,241] [INFO] Query marker FASTA was written to GCF_000374585.1_ASM37458v1_genomic.fna/markers.fasta
[2024-01-24 13:28:49,242] [INFO] Task started: Blastn
[2024-01-24 13:28:49,242] [INFO] Running command: blastn -query GCF_000374585.1_ASM37458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13055dfd-503e-49ee-b100-1af9d5049f2e/dqc_reference/reference_markers.fasta -out GCF_000374585.1_ASM37458v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:49,960] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:49,964] [INFO] Selected 13 target genomes.
[2024-01-24 13:28:49,965] [INFO] Target genome list was writen to GCF_000374585.1_ASM37458v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:49,977] [INFO] Task started: fastANI
[2024-01-24 13:28:49,977] [INFO] Running command: fastANI --query /var/lib/cwl/stg40e766f4-677a-41a6-b4b4-363c1bc45b3c/GCF_000374585.1_ASM37458v1_genomic.fna.gz --refList GCF_000374585.1_ASM37458v1_genomic.fna/target_genomes.txt --output GCF_000374585.1_ASM37458v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:59,863] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:59,863] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13055dfd-503e-49ee-b100-1af9d5049f2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:59,864] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13055dfd-503e-49ee-b100-1af9d5049f2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:59,874] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:28:59,874] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:59,875] [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
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	100.0	1181	1183	95	conclusive
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	99.9651	1165	1183	95	conclusive
Phocaeicola coprocola	strain=DSM 17136	GCA_000154845.1	310298	310298	suspected-type	True	81.0623	315	1183	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	80.4049	403	1183	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	80.3817	413	1183	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	80.2043	153	1183	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	80.1074	301	1183	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	79.958	363	1183	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	79.7909	369	1183	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	79.6192	191	1183	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	79.5467	174	1183	95	below_threshold
Phocaeicola sartorii	strain=DSM 21941	GCA_024622025.1	671267	671267	type	True	78.0123	225	1183	95	below_threshold
Bacteroides cellulosilyticus	strain=DSM 14838	GCA_000158035.1	246787	246787	type	True	77.4844	149	1183	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:59,876] [INFO] DFAST Taxonomy check result was written to GCF_000374585.1_ASM37458v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:59,877] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:59,877] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:59,877] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13055dfd-503e-49ee-b100-1af9d5049f2e/dqc_reference/checkm_data
[2024-01-24 13:28:59,878] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:59,915] [INFO] Task started: CheckM
[2024-01-24 13:28:59,916] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000374585.1_ASM37458v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000374585.1_ASM37458v1_genomic.fna/checkm_input GCF_000374585.1_ASM37458v1_genomic.fna/checkm_result
[2024-01-24 13:29:55,558] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:55,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:55,574] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:55,574] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:55,575] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000374585.1_ASM37458v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:55,575] [INFO] Task started: Blastn
[2024-01-24 13:29:55,575] [INFO] Running command: blastn -query GCF_000374585.1_ASM37458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13055dfd-503e-49ee-b100-1af9d5049f2e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000374585.1_ASM37458v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:56,576] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:56,580] [INFO] Selected 17 target genomes.
[2024-01-24 13:29:56,581] [INFO] Target genome list was writen to GCF_000374585.1_ASM37458v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:56,594] [INFO] Task started: fastANI
[2024-01-24 13:29:56,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg40e766f4-677a-41a6-b4b4-363c1bc45b3c/GCF_000374585.1_ASM37458v1_genomic.fna.gz --refList GCF_000374585.1_ASM37458v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000374585.1_ASM37458v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:07,210] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:07,224] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:07,224] [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_000374585.1	s__Phocaeicola barnesiae	100.0	1181	1183	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.58	98.10	0.88	0.84	8	conclusive
GCA_900551645.1	s__Phocaeicola sp900551645	88.874	568	1183	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.46	98.46	0.80	0.80	2	-
GCA_900553185.1	s__Phocaeicola sp900553185	83.7775	496	1183	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.97	99.95	0.91	0.85	3	-
GCA_902362595.1	s__Phocaeicola merdigallinarum	81.132	435	1183	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	96.40	0.87	0.80	6	-
GCF_003437535.1	s__Phocaeicola plebeius_A	81.0337	416	1183	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.72	95.85	0.84	0.73	27	-
GCF_900128455.1	s__Phocaeicola mediterraneensis	80.5941	453	1183	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.66	98.61	0.84	0.80	3	-
GCF_013618865.1	s__Phocaeicola sp900541515	80.4315	410	1183	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.28	99.22	0.94	0.91	4	-
GCF_000187895.1	s__Phocaeicola plebeius	80.3896	404	1183	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.22	96.70	0.79	0.55	12	-
GCF_900128495.1	s__Phocaeicola ilei	80.0659	389	1183	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.42	98.42	0.92	0.92	2	-
GCA_900551445.1	s__Phocaeicola sp900551445	79.7243	319	1183	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.87	97.79	0.75	0.72	3	-
GCA_900552075.1	s__Phocaeicola sp900552075	79.6575	296	1183	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000432735.1	s__Phocaeicola sp000432735	79.1753	340	1183	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.41	98.37	0.86	0.85	3	-
GCA_900542985.1	s__Phocaeicola sp900542985	79.0204	233	1183	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.63	98.57	0.79	0.72	3	-
GCF_016899805.1	s__Phocaeicola gallinaceus	78.8951	284	1183	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.20	97.80	0.80	0.74	12	-
GCA_000436795.1	s__Phocaeicola sp000436795	78.3706	249	1183	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.87	99.87	0.96	0.96	3	-
GCA_019120125.1	s__Phocaeicola excrementigallinarum	77.8828	273	1183	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004558305.1	s__Phocaeicola plebeius_B	77.7848	217	1183	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:07,226] [INFO] GTDB search result was written to GCF_000374585.1_ASM37458v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:07,226] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:07,230] [INFO] DFAST_QC result json was written to GCF_000374585.1_ASM37458v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:07,230] [INFO] DFAST_QC completed!
[2024-01-24 13:30:07,230] [INFO] Total running time: 0h1m38s