[2024-01-24 10:47:54,166] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:54,459] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:54,460] [INFO] DQC Reference Directory: /var/lib/cwl/stg952fe9c0-5fd6-4eb7-b2be-940235a36f06/dqc_reference
[2024-01-24 10:48:03,343] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:03,345] [INFO] Task started: Prodigal
[2024-01-24 10:48:03,346] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7131396-b3f3-4af1-be70-8cfc5f12d322/GCF_014337215.1_ASM1433721v1_genomic.fna.gz | prodigal -d GCF_014337215.1_ASM1433721v1_genomic.fna/cds.fna -a GCF_014337215.1_ASM1433721v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:13,355] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:13,355] [INFO] Task started: HMMsearch
[2024-01-24 10:48:13,355] [INFO] Running command: hmmsearch --tblout GCF_014337215.1_ASM1433721v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg952fe9c0-5fd6-4eb7-b2be-940235a36f06/dqc_reference/reference_markers.hmm GCF_014337215.1_ASM1433721v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:13,641] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:13,643] [INFO] Found 6/6 markers.
[2024-01-24 10:48:13,690] [INFO] Query marker FASTA was written to GCF_014337215.1_ASM1433721v1_genomic.fna/markers.fasta
[2024-01-24 10:48:13,691] [INFO] Task started: Blastn
[2024-01-24 10:48:13,691] [INFO] Running command: blastn -query GCF_014337215.1_ASM1433721v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg952fe9c0-5fd6-4eb7-b2be-940235a36f06/dqc_reference/reference_markers.fasta -out GCF_014337215.1_ASM1433721v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:14,335] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:14,339] [INFO] Selected 23 target genomes.
[2024-01-24 10:48:14,339] [INFO] Target genome list was writen to GCF_014337215.1_ASM1433721v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:14,362] [INFO] Task started: fastANI
[2024-01-24 10:48:14,362] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7131396-b3f3-4af1-be70-8cfc5f12d322/GCF_014337215.1_ASM1433721v1_genomic.fna.gz --refList GCF_014337215.1_ASM1433721v1_genomic.fna/target_genomes.txt --output GCF_014337215.1_ASM1433721v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:29,127] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:29,128] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg952fe9c0-5fd6-4eb7-b2be-940235a36f06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:29,128] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg952fe9c0-5fd6-4eb7-b2be-940235a36f06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:29,142] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:29,142] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:29,142] [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
Wansuia hejianensis	strain=NSJ-29	GCA_014337215.1	2763667	2763667	type	True	100.0	1316	1316	95	conclusive
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	81.763	62	1316	95	below_threshold
Sporofaciens musculi	strain=WCA-9-b2	GCA_009830285.1	2681861	2681861	type	True	81.3977	69	1316	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	80.6395	52	1316	95	below_threshold
Lactonifactor longoviformis	strain=DSM 17459	GCA_900129135.1	341220	341220	suspected-type	True	79.3619	81	1316	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	78.9782	58	1316	95	below_threshold
Luxibacter massiliensis	strain=Marseille-P5551	GCA_900604355.1	2219695	2219695	type	True	78.9553	61	1316	95	below_threshold
Blautia argi	strain=KCTC 15426	GCA_003287895.1	1912897	1912897	type	True	78.4272	73	1316	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	78.0716	61	1316	95	below_threshold
Lactonifactor longoviformis	strain=DSM 17459	GCA_002915525.1	341220	341220	suspected-type	True	77.9325	66	1316	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	77.8306	62	1316	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_025151995.1	438033	438033	type	True	77.5279	94	1316	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_000425525.1	438033	438033	type	True	77.0924	96	1316	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	76.5629	65	1316	95	below_threshold
Cuneatibacter caecimuris	strain=DSM 29486	GCA_004216775.1	1796618	1796618	type	True	76.3588	57	1316	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:29,144] [INFO] DFAST Taxonomy check result was written to GCF_014337215.1_ASM1433721v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:29,144] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:29,145] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:29,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg952fe9c0-5fd6-4eb7-b2be-940235a36f06/dqc_reference/checkm_data
[2024-01-24 10:48:29,146] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:29,188] [INFO] Task started: CheckM
[2024-01-24 10:48:29,188] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014337215.1_ASM1433721v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014337215.1_ASM1433721v1_genomic.fna/checkm_input GCF_014337215.1_ASM1433721v1_genomic.fna/checkm_result
[2024-01-24 10:49:03,527] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:03,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:03,553] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:03,553] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:03,554] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014337215.1_ASM1433721v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:03,554] [INFO] Task started: Blastn
[2024-01-24 10:49:03,554] [INFO] Running command: blastn -query GCF_014337215.1_ASM1433721v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg952fe9c0-5fd6-4eb7-b2be-940235a36f06/dqc_reference/reference_markers_gtdb.fasta -out GCF_014337215.1_ASM1433721v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:04,661] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:04,667] [INFO] Selected 25 target genomes.
[2024-01-24 10:49:04,667] [INFO] Target genome list was writen to GCF_014337215.1_ASM1433721v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:04,723] [INFO] Task started: fastANI
[2024-01-24 10:49:04,724] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7131396-b3f3-4af1-be70-8cfc5f12d322/GCF_014337215.1_ASM1433721v1_genomic.fna.gz --refList GCF_014337215.1_ASM1433721v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014337215.1_ASM1433721v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:19,361] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:19,382] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:19,383] [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_014337215.1	s__Scatomonas sp003481995	100.0	1316	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Scatomonas	95.0	99.67	99.67	0.93	0.93	3	conclusive
GCF_900129135.1	s__Lactonifactor longoviformis	79.3579	81	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lactonifactor	95.0	99.99	99.99	0.99	0.99	3	-
GCF_900604355.1	s__Luxibacter massiliensis	79.2911	60	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Luxibacter	95.0	99.05	99.03	0.91	0.91	3	-
GCF_013302405.1	s__Blautia_A caecimuris	79.1156	75	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.97	96.45	0.87	0.70	11	-
GCA_018716575.1	s__Scatomonas merdavium	78.3776	262	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Scatomonas	95.0	98.69	98.69	0.82	0.82	2	-
GCF_009707925.1	s__Blautia_A luti	78.056	62	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.33	97.04	0.87	0.84	5	-
GCA_018716305.1	s__Scatomonas merdigallinarum	78.0241	166	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Scatomonas	95.0	99.11	99.10	0.93	0.92	3	-
GCF_016899975.1	s__Fusicatenibacter sp900543115	77.7306	115	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter	95.0	98.27	97.10	0.88	0.78	8	-
GCA_018713515.1	s__Scatomonas pullistercoris	77.6196	181	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Scatomonas	95.0	99.97	99.97	0.94	0.94	2	-
GCA_003478355.1	s__UBA3402 sp003478355	77.2473	54	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	97.92	96.21	0.85	0.69	6	-
GCA_018374355.1	s__Oliverpabstia sp018374355	77.1174	75	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425525.1	s__Ruminococcus_G gauvreauii	77.0869	96	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_G	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900539175.1	s__Pelethocola sp900539175	76.8858	107	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pelethocola	95.0	99.69	99.49	0.84	0.76	3	-
GCA_018713585.1	s__Pullilachnospira stercoravium	76.7996	81	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pullilachnospira	95.0	97.91	97.84	0.85	0.79	6	-
GCA_900542045.1	s__Blautia_A gallistercoris	76.714	83	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.42	98.42	0.88	0.88	2	-
GCA_018711275.1	s__Pullilachnospira intestinigallinarum	76.462	91	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pullilachnospira	95.0	99.92	99.92	0.90	0.90	2	-
GCA_018711815.1	s__Egerieimonas intestinavium	76.4468	81	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Egerieimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216775.1	s__Cuneatibacter caecimuris	76.2739	59	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Cuneatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905201705.1	s__Marvinbryantia sp900550755	76.09	73	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	99.85	99.71	0.93	0.91	3	-
GCA_910588285.1	s__14-2 sp910588285	75.8525	61	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009774255.1	s__Schaedlerella sp009774255	75.8212	68	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:19,384] [INFO] GTDB search result was written to GCF_014337215.1_ASM1433721v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:19,385] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:19,389] [INFO] DFAST_QC result json was written to GCF_014337215.1_ASM1433721v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:19,389] [INFO] DFAST_QC completed!
[2024-01-24 10:49:19,390] [INFO] Total running time: 0h1m25s