[2024-01-24 11:05:03,933] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,937] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,937] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f7750af-7cb7-4989-93b3-6785e9509aee/dqc_reference
[2024-01-24 11:05:05,811] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,812] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,813] [INFO] Running command: gunzip -c /var/lib/cwl/stgd06cd737-9c24-471e-878c-6d6d2c3879f8/GCF_014287625.1_ASM1428762v1_genomic.fna.gz | prodigal -d GCF_014287625.1_ASM1428762v1_genomic.fna/cds.fna -a GCF_014287625.1_ASM1428762v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:13,155] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:13,155] [INFO] Task started: HMMsearch
[2024-01-24 11:05:13,155] [INFO] Running command: hmmsearch --tblout GCF_014287625.1_ASM1428762v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f7750af-7cb7-4989-93b3-6785e9509aee/dqc_reference/reference_markers.hmm GCF_014287625.1_ASM1428762v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:13,486] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:13,487] [INFO] Found 6/6 markers.
[2024-01-24 11:05:13,516] [INFO] Query marker FASTA was written to GCF_014287625.1_ASM1428762v1_genomic.fna/markers.fasta
[2024-01-24 11:05:13,516] [INFO] Task started: Blastn
[2024-01-24 11:05:13,516] [INFO] Running command: blastn -query GCF_014287625.1_ASM1428762v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f7750af-7cb7-4989-93b3-6785e9509aee/dqc_reference/reference_markers.fasta -out GCF_014287625.1_ASM1428762v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:14,137] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:14,146] [INFO] Selected 28 target genomes.
[2024-01-24 11:05:14,146] [INFO] Target genome list was writen to GCF_014287625.1_ASM1428762v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:14,156] [INFO] Task started: fastANI
[2024-01-24 11:05:14,156] [INFO] Running command: fastANI --query /var/lib/cwl/stgd06cd737-9c24-471e-878c-6d6d2c3879f8/GCF_014287625.1_ASM1428762v1_genomic.fna.gz --refList GCF_014287625.1_ASM1428762v1_genomic.fna/target_genomes.txt --output GCF_014287625.1_ASM1428762v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:30,385] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:30,386] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f7750af-7cb7-4989-93b3-6785e9509aee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:30,386] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f7750af-7cb7-4989-93b3-6785e9509aee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:30,397] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:05:30,397] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:05:30,398] [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	81.952	121	1068	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	81.8187	116	1068	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	81.585	87	1068	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	79.3963	93	1068	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	79.1175	96	1068	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	79.0773	105	1068	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002234575.2	208479	208479	type	True	78.8799	98	1068	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	78.8756	99	1068	95	below_threshold
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	78.4866	118	1068	95	below_threshold
Diplocloster modestus	strain=ASD4241	GCA_019042245.1	2850322	2850322	type	True	78.4297	69	1068	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	78.0727	106	1068	95	below_threshold
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	78.0602	105	1068	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_000173815.1	168384	168384	type	True	78.0232	107	1068	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	77.5351	92	1068	95	below_threshold
Wansuia hejianensis	strain=NSJ-29	GCA_014337215.1	2763667	2763667	type	True	76.8559	67	1068	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	76.8469	77	1068	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	76.7945	79	1068	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_000425525.1	438033	438033	type	True	76.5909	54	1068	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_025151995.1	438033	438033	type	True	76.506	53	1068	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:30,399] [INFO] DFAST Taxonomy check result was written to GCF_014287625.1_ASM1428762v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:30,399] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:30,399] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:30,400] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f7750af-7cb7-4989-93b3-6785e9509aee/dqc_reference/checkm_data
[2024-01-24 11:05:30,400] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:30,435] [INFO] Task started: CheckM
[2024-01-24 11:05:30,435] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014287625.1_ASM1428762v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014287625.1_ASM1428762v1_genomic.fna/checkm_input GCF_014287625.1_ASM1428762v1_genomic.fna/checkm_result
[2024-01-24 11:05:55,723] [INFO] Task succeeded: CheckM
[2024-01-24 11:05:55,724] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:05:55,740] [INFO] ===== Completeness check finished =====
[2024-01-24 11:05:55,741] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:05:55,741] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014287625.1_ASM1428762v1_genomic.fna/markers.fasta)
[2024-01-24 11:05:55,741] [INFO] Task started: Blastn
[2024-01-24 11:05:55,741] [INFO] Running command: blastn -query GCF_014287625.1_ASM1428762v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f7750af-7cb7-4989-93b3-6785e9509aee/dqc_reference/reference_markers_gtdb.fasta -out GCF_014287625.1_ASM1428762v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:56,858] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:56,861] [INFO] Selected 15 target genomes.
[2024-01-24 11:05:56,861] [INFO] Target genome list was writen to GCF_014287625.1_ASM1428762v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:05:56,870] [INFO] Task started: fastANI
[2024-01-24 11:05:56,870] [INFO] Running command: fastANI --query /var/lib/cwl/stgd06cd737-9c24-471e-878c-6d6d2c3879f8/GCF_014287625.1_ASM1428762v1_genomic.fna.gz --refList GCF_014287625.1_ASM1428762v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014287625.1_ASM1428762v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:06,846] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:06,856] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:06,856] [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_014290175.1	s__Merdisoma sp014290175	99.9939	1067	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	99.98	99.96	0.81	0.62	3	conclusive
GCA_902362725.1	s__Merdisoma sp900066385	86.8516	673	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	98.97	97.93	0.91	0.83	3	-
GCA_900553635.1	s__Merdisoma sp900553635	85.8086	444	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	97.48	97.13	0.82	0.78	3	-
GCF_002160765.1	s__Merdisoma faecalis	79.0827	347	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	98.59	98.32	0.91	0.81	8	-
GCF_002160825.1	s__Merdisoma sp002160825	79.0708	337	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	99.04	99.04	0.92	0.92	2	-
GCA_009917555.1	s__Merdisoma sp009917555	78.5418	240	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	99.22	99.22	0.93	0.93	2	-
GCA_018715645.1	s__Merdisoma merdipullorum	78.3638	271	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	99.92	99.92	0.91	0.91	2	-
GCA_910574835.1	s__Merdisoma sp910574835	78.309	205	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014385265.1	s__Copromonas sp000435795	77.7689	102	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	98.24	96.73	0.89	0.84	6	-
GCA_910575725.1	s__Merdisoma sp011959465	77.7203	248	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	99.24	98.50	0.89	0.80	3	-
GCA_910574255.1	s__Merdisoma sp910574255	77.7115	201	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	98.74	98.74	0.82	0.82	2	-
GCA_910586955.1	s__Merdisoma sp910586955	77.3071	204	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018711815.1	s__Egerieimonas intestinavium	77.1698	115	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Egerieimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549235.1	s__Enterocloster sp900549235	76.9109	95	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.03	99.00	0.79	0.77	3	-
GCA_905215775.1	s__Copromonas sp905215775	76.2479	83	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:06,857] [INFO] GTDB search result was written to GCF_014287625.1_ASM1428762v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:06,858] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:06,861] [INFO] DFAST_QC result json was written to GCF_014287625.1_ASM1428762v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:06,861] [INFO] DFAST_QC completed!
[2024-01-24 11:06:06,861] [INFO] Total running time: 0h1m3s