[2024-01-24 11:12:57,973] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:57,974] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:57,974] [INFO] DQC Reference Directory: /var/lib/cwl/stg6103b536-8fbd-4dbf-9141-f14c470813f7/dqc_reference
[2024-01-24 11:12:59,321] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:59,322] [INFO] Task started: Prodigal
[2024-01-24 11:12:59,323] [INFO] Running command: gunzip -c /var/lib/cwl/stg13ae8115-34d0-44f3-9f7a-c0c5595f77bd/GCF_014297245.1_ASM1429724v1_genomic.fna.gz | prodigal -d GCF_014297245.1_ASM1429724v1_genomic.fna/cds.fna -a GCF_014297245.1_ASM1429724v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:07,591] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:07,592] [INFO] Task started: HMMsearch
[2024-01-24 11:13:07,592] [INFO] Running command: hmmsearch --tblout GCF_014297245.1_ASM1429724v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6103b536-8fbd-4dbf-9141-f14c470813f7/dqc_reference/reference_markers.hmm GCF_014297245.1_ASM1429724v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:07,902] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:07,903] [INFO] Found 6/6 markers.
[2024-01-24 11:13:07,954] [INFO] Query marker FASTA was written to GCF_014297245.1_ASM1429724v1_genomic.fna/markers.fasta
[2024-01-24 11:13:07,954] [INFO] Task started: Blastn
[2024-01-24 11:13:07,955] [INFO] Running command: blastn -query GCF_014297245.1_ASM1429724v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6103b536-8fbd-4dbf-9141-f14c470813f7/dqc_reference/reference_markers.fasta -out GCF_014297245.1_ASM1429724v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:08,636] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:08,639] [INFO] Selected 17 target genomes.
[2024-01-24 11:13:08,640] [INFO] Target genome list was writen to GCF_014297245.1_ASM1429724v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:08,646] [INFO] Task started: fastANI
[2024-01-24 11:13:08,646] [INFO] Running command: fastANI --query /var/lib/cwl/stg13ae8115-34d0-44f3-9f7a-c0c5595f77bd/GCF_014297245.1_ASM1429724v1_genomic.fna.gz --refList GCF_014297245.1_ASM1429724v1_genomic.fna/target_genomes.txt --output GCF_014297245.1_ASM1429724v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:21,138] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:21,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6103b536-8fbd-4dbf-9141-f14c470813f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:21,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6103b536-8fbd-4dbf-9141-f14c470813f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:21,152] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:13:21,152] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:13:21,152] [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
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	87.5346	737	1156	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	87.4212	699	1156	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	85.6197	630	1156	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	82.0298	369	1156	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	81.9615	361	1156	95	below_threshold
Jutongia huaianensis	strain=NSJ-37	GCA_014384985.1	2763668	2763668	type	True	81.9587	90	1156	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	81.6843	333	1156	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	81.2712	386	1156	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	81.0409	163	1156	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	80.8812	192	1156	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	79.4132	299	1156	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	78.495	80	1156	95	below_threshold
Anaerostipes faecalis	strain=AGMB03513	GCA_018982945.1	2738446	2738446	type	True	77.8555	56	1156	95	below_threshold
Blautia hydrogenotrophica	strain=DSM 10507	GCA_000157975.1	53443	53443	type	True	77.381	83	1156	95	below_threshold
Lacrimispora celerecrescens	strain=18A	GCA_002797975.1	29354	29354	type	True	76.2602	51	1156	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:21,154] [INFO] DFAST Taxonomy check result was written to GCF_014297245.1_ASM1429724v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:21,154] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:21,154] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:21,154] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6103b536-8fbd-4dbf-9141-f14c470813f7/dqc_reference/checkm_data
[2024-01-24 11:13:21,155] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:21,197] [INFO] Task started: CheckM
[2024-01-24 11:13:21,197] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014297245.1_ASM1429724v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014297245.1_ASM1429724v1_genomic.fna/checkm_input GCF_014297245.1_ASM1429724v1_genomic.fna/checkm_result
[2024-01-24 11:13:52,638] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:52,640] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:52,661] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:52,661] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:52,661] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014297245.1_ASM1429724v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:52,662] [INFO] Task started: Blastn
[2024-01-24 11:13:52,662] [INFO] Running command: blastn -query GCF_014297245.1_ASM1429724v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6103b536-8fbd-4dbf-9141-f14c470813f7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014297245.1_ASM1429724v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:53,687] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:53,690] [INFO] Selected 8 target genomes.
[2024-01-24 11:13:53,691] [INFO] Target genome list was writen to GCF_014297245.1_ASM1429724v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:53,696] [INFO] Task started: fastANI
[2024-01-24 11:13:53,697] [INFO] Running command: fastANI --query /var/lib/cwl/stg13ae8115-34d0-44f3-9f7a-c0c5595f77bd/GCF_014297245.1_ASM1429724v1_genomic.fna.gz --refList GCF_014297245.1_ASM1429724v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014297245.1_ASM1429724v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:01,467] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:01,480] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:01,481] [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_000285855.2	s__Blautia_A sp000285855	97.8227	965	1156	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.62	95.80	0.88	0.79	6	conclusive
GCF_013300825.1	s__Blautia_A wexlerae_B	87.5592	665	1156	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.68	98.07	0.89	0.86	5	-
GCF_000484655.1	s__Blautia_A wexlerae	87.5062	693	1156	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.38	96.15	0.76	0.65	140	-
GCF_003471165.1	s__Blautia_A sp003471165	87.0543	721	1156	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.40	97.74	0.83	0.79	20	-
GCF_009707925.1	s__Blautia_A luti	85.6296	630	1156	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	-
GCF_003477525.1	s__Blautia_A sp003477525	85.3309	654	1156	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.30	98.60	0.90	0.81	3	-
GCA_905209435.1	s__Blautia_A sp905209435	81.9143	485	1156	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013304385.1	s__Blautia_A sp900066505	80.6787	288	1156	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.06	97.97	0.82	0.78	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:01,482] [INFO] GTDB search result was written to GCF_014297245.1_ASM1429724v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:01,483] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:01,488] [INFO] DFAST_QC result json was written to GCF_014297245.1_ASM1429724v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:01,488] [INFO] DFAST_QC completed!
[2024-01-24 11:14:01,489] [INFO] Total running time: 0h1m4s