[2023-06-13 00:37:00,203] [INFO] DFAST_QC pipeline started.
[2023-06-13 00:37:00,225] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 00:37:00,225] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4ec6914-ed9e-4c5f-99e4-cf0806a9e0e4/dqc_reference
[2023-06-13 00:37:02,059] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 00:37:02,060] [INFO] Task started: Prodigal
[2023-06-13 00:37:02,060] [INFO] Running command: gunzip -c /var/lib/cwl/stg403da4cc-dc33-4ba5-bb58-58311551d9c5/GCA_022738855.1_ASM2273885v1_genomic.fna.gz | prodigal -d GCA_022738855.1_ASM2273885v1_genomic.fna/cds.fna -a GCA_022738855.1_ASM2273885v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 00:37:17,813] [INFO] Task succeeded: Prodigal
[2023-06-13 00:37:17,814] [INFO] Task started: HMMsearch
[2023-06-13 00:37:17,814] [INFO] Running command: hmmsearch --tblout GCA_022738855.1_ASM2273885v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4ec6914-ed9e-4c5f-99e4-cf0806a9e0e4/dqc_reference/reference_markers.hmm GCA_022738855.1_ASM2273885v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 00:37:18,060] [INFO] Task succeeded: HMMsearch
[2023-06-13 00:37:18,061] [INFO] Found 6/6 markers.
[2023-06-13 00:37:18,092] [INFO] Query marker FASTA was written to GCA_022738855.1_ASM2273885v1_genomic.fna/markers.fasta
[2023-06-13 00:37:18,092] [INFO] Task started: Blastn
[2023-06-13 00:37:18,093] [INFO] Running command: blastn -query GCA_022738855.1_ASM2273885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4ec6914-ed9e-4c5f-99e4-cf0806a9e0e4/dqc_reference/reference_markers.fasta -out GCA_022738855.1_ASM2273885v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:37:18,684] [INFO] Task succeeded: Blastn
[2023-06-13 00:37:18,689] [INFO] Selected 17 target genomes.
[2023-06-13 00:37:18,689] [INFO] Target genome list was writen to GCA_022738855.1_ASM2273885v1_genomic.fna/target_genomes.txt
[2023-06-13 00:37:18,700] [INFO] Task started: fastANI
[2023-06-13 00:37:18,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg403da4cc-dc33-4ba5-bb58-58311551d9c5/GCA_022738855.1_ASM2273885v1_genomic.fna.gz --refList GCA_022738855.1_ASM2273885v1_genomic.fna/target_genomes.txt --output GCA_022738855.1_ASM2273885v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 00:37:26,909] [INFO] Task succeeded: fastANI
[2023-06-13 00:37:26,910] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4ec6914-ed9e-4c5f-99e4-cf0806a9e0e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 00:37:26,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4ec6914-ed9e-4c5f-99e4-cf0806a9e0e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 00:37:26,925] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 00:37:26,925] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 00:37:26,925] [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
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	97.2199	738	868	95	conclusive
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	81.2223	401	868	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	81.1903	396	868	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	81.0622	415	868	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	77.669	86	868	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	77.3774	103	868	95	below_threshold
Prevotella melaninogenica	strain=FDAARGOS_1566	GCA_020735785.1	28132	28132	suspected-type	True	77.1093	73	868	95	below_threshold
Prevotella scopos	strain=W2052	GCA_001683355.1	589437	589437	type	True	77.0071	63	868	95	below_threshold
Prevotella scopos	strain=W2052	GCA_018127785.1	589437	589437	type	True	76.9665	64	868	95	below_threshold
Prevotella scopos	strain=DSM 22613	GCA_900129535.1	589437	589437	type	True	76.9296	65	868	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.4904	58	868	95	below_threshold
Prevotella herbatica	strain=WR041	GCA_017347605.1	2801997	2801997	type	True	76.3485	71	868	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 00:37:26,928] [INFO] DFAST Taxonomy check result was written to GCA_022738855.1_ASM2273885v1_genomic.fna/tc_result.tsv
[2023-06-13 00:37:26,928] [INFO] ===== Taxonomy check completed =====
[2023-06-13 00:37:26,929] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 00:37:26,929] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4ec6914-ed9e-4c5f-99e4-cf0806a9e0e4/dqc_reference/checkm_data
[2023-06-13 00:37:26,930] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 00:37:26,963] [INFO] Task started: CheckM
[2023-06-13 00:37:26,963] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022738855.1_ASM2273885v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022738855.1_ASM2273885v1_genomic.fna/checkm_input GCA_022738855.1_ASM2273885v1_genomic.fna/checkm_result
[2023-06-13 00:38:15,091] [INFO] Task succeeded: CheckM
[2023-06-13 00:38:15,093] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.84%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 00:38:15,114] [INFO] ===== Completeness check finished =====
[2023-06-13 00:38:15,114] [INFO] ===== Start GTDB Search =====
[2023-06-13 00:38:15,115] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022738855.1_ASM2273885v1_genomic.fna/markers.fasta)
[2023-06-13 00:38:15,115] [INFO] Task started: Blastn
[2023-06-13 00:38:15,115] [INFO] Running command: blastn -query GCA_022738855.1_ASM2273885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4ec6914-ed9e-4c5f-99e4-cf0806a9e0e4/dqc_reference/reference_markers_gtdb.fasta -out GCA_022738855.1_ASM2273885v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:38:15,966] [INFO] Task succeeded: Blastn
[2023-06-13 00:38:15,971] [INFO] Selected 16 target genomes.
[2023-06-13 00:38:15,971] [INFO] Target genome list was writen to GCA_022738855.1_ASM2273885v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 00:38:15,973] [INFO] Task started: fastANI
[2023-06-13 00:38:15,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg403da4cc-dc33-4ba5-bb58-58311551d9c5/GCA_022738855.1_ASM2273885v1_genomic.fna.gz --refList GCA_022738855.1_ASM2273885v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022738855.1_ASM2273885v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 00:38:25,807] [INFO] Task succeeded: fastANI
[2023-06-13 00:38:25,826] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 00:38:25,826] [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_004535825.1	s__Prevotella hominis	97.2473	737	868	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.52	95.16	0.76	0.66	13	conclusive
GCA_900554835.1	s__Prevotella sp900554835	94.3619	626	868	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019127135.1	s__Prevotella sp900551275	81.6071	412	868	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0063	98.12	96.96	0.86	0.77	7	-
GCF_009494395.1	s__Prevotella sp900546535	81.5822	425	868	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.78	96.11	0.82	0.79	8	-
GCA_900544825.1	s__Prevotella sp900544825	81.55	385	868	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.36	98.76	0.90	0.84	3	-
GCF_015074785.1	s__Prevotella sp015074785	81.5467	434	868	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.50	95.88	0.80	0.71	45	-
GCA_900551985.1	s__Prevotella sp900551985	81.5258	354	868	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.28	99.28	0.87	0.87	2	-
GCA_019249655.1	s__Prevotella sp900767615	81.4917	456	868	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.47	95.77	0.82	0.75	7	-
GCA_000436035.1	s__Prevotella sp000436035	81.4457	389	868	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.58	97.92	0.86	0.81	4	-
GCF_000157935.1	s__Prevotella copri	81.2296	401	868	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	-
GCA_900557035.1	s__Prevotella sp900557035	81.032	304	868	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.84	97.17	0.78	0.68	3	-
GCA_002451555.1	s__Prevotella sp002451555	80.7874	386	868	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.47	99.47	0.85	0.85	2	-
GCA_900555035.1	s__Prevotella sp900555035	80.6865	367	868	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009495355.1	s__Prevotella sp900313215	80.4186	329	868	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.34	96.92	0.81	0.74	15	-
GCA_900548535.1	s__Prevotella sp900548535	80.3396	317	868	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440225.1	s__Prevotella sp002440225	79.6995	285	868	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.88	98.88	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-06-13 00:38:25,828] [INFO] GTDB search result was written to GCA_022738855.1_ASM2273885v1_genomic.fna/result_gtdb.tsv
[2023-06-13 00:38:25,829] [INFO] ===== GTDB Search completed =====
[2023-06-13 00:38:25,832] [INFO] DFAST_QC result json was written to GCA_022738855.1_ASM2273885v1_genomic.fna/dqc_result.json
[2023-06-13 00:38:25,833] [INFO] DFAST_QC completed!
[2023-06-13 00:38:25,833] [INFO] Total running time: 0h1m26s