[2024-01-24 12:37:37,924] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:37,926] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:37,927] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ac42b6a-73fa-4091-83fa-8daaba0c81e7/dqc_reference
[2024-01-24 12:37:41,016] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:41,017] [INFO] Task started: Prodigal
[2024-01-24 12:37:41,017] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b55cbbb-571f-4a67-ac29-172b2cb10381/GCF_013409575.1_ASM1340957v1_genomic.fna.gz | prodigal -d GCF_013409575.1_ASM1340957v1_genomic.fna/cds.fna -a GCF_013409575.1_ASM1340957v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:58,945] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:58,946] [INFO] Task started: HMMsearch
[2024-01-24 12:37:58,946] [INFO] Running command: hmmsearch --tblout GCF_013409575.1_ASM1340957v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ac42b6a-73fa-4091-83fa-8daaba0c81e7/dqc_reference/reference_markers.hmm GCF_013409575.1_ASM1340957v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:59,224] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:59,227] [INFO] Found 6/6 markers.
[2024-01-24 12:37:59,264] [INFO] Query marker FASTA was written to GCF_013409575.1_ASM1340957v1_genomic.fna/markers.fasta
[2024-01-24 12:37:59,264] [INFO] Task started: Blastn
[2024-01-24 12:37:59,264] [INFO] Running command: blastn -query GCF_013409575.1_ASM1340957v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ac42b6a-73fa-4091-83fa-8daaba0c81e7/dqc_reference/reference_markers.fasta -out GCF_013409575.1_ASM1340957v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:59,880] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:59,884] [INFO] Selected 20 target genomes.
[2024-01-24 12:37:59,885] [INFO] Target genome list was writen to GCF_013409575.1_ASM1340957v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:59,927] [INFO] Task started: fastANI
[2024-01-24 12:37:59,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b55cbbb-571f-4a67-ac29-172b2cb10381/GCF_013409575.1_ASM1340957v1_genomic.fna.gz --refList GCF_013409575.1_ASM1340957v1_genomic.fna/target_genomes.txt --output GCF_013409575.1_ASM1340957v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:13,890] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:13,891] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ac42b6a-73fa-4091-83fa-8daaba0c81e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:13,891] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ac42b6a-73fa-4091-83fa-8daaba0c81e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:13,906] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:38:13,906] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:38:13,906] [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
Parabacteroides johnsonii	strain=DSM 18315	GCA_025151045.1	387661	387661	type	True	78.9153	130	1306	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	78.6549	130	1306	95	below_threshold
Parabacteroides gordonii	strain=FDAARGOS_1522	GCA_020297465.1	574930	574930	type	True	78.0394	176	1306	95	below_threshold
Parabacteroides timonensis	strain=Marseille-P3236	GCA_900128505.1	1871013	1871013	type	True	77.9699	165	1306	95	below_threshold
Parabacteroides goldsteinii	strain=DSM 19448	GCA_000969835.1	328812	328812	type	True	77.9599	168	1306	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_000156495.1	387661	387661	type	True	77.9551	123	1306	95	below_threshold
Parabacteroides gordonii	strain=MS-1	GCA_000969825.1	574930	574930	type	True	77.932	174	1306	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_000154105.1	46503	46503	type	True	77.9092	123	1306	95	below_threshold
Parabacteroides faecis	strain=DSM 102983	GCA_014199665.1	1217282	1217282	type	True	77.5468	174	1306	95	below_threshold
Parabacteroides gordonii	strain=DSM 23371	GCA_000428565.1	574930	574930	type	True	77.5175	173	1306	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	77.1834	59	1306	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	76.2584	50	1306	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	76.1453	51	1306	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:13,914] [INFO] DFAST Taxonomy check result was written to GCF_013409575.1_ASM1340957v1_genomic.fna/tc_result.tsv
[2024-01-24 12:38:13,915] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:13,915] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:13,915] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ac42b6a-73fa-4091-83fa-8daaba0c81e7/dqc_reference/checkm_data
[2024-01-24 12:38:13,917] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:13,970] [INFO] Task started: CheckM
[2024-01-24 12:38:13,970] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013409575.1_ASM1340957v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013409575.1_ASM1340957v1_genomic.fna/checkm_input GCF_013409575.1_ASM1340957v1_genomic.fna/checkm_result
[2024-01-24 12:39:06,389] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:06,391] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:06,413] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:06,414] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:06,414] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013409575.1_ASM1340957v1_genomic.fna/markers.fasta)
[2024-01-24 12:39:06,415] [INFO] Task started: Blastn
[2024-01-24 12:39:06,415] [INFO] Running command: blastn -query GCF_013409575.1_ASM1340957v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ac42b6a-73fa-4091-83fa-8daaba0c81e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_013409575.1_ASM1340957v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:07,284] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:07,289] [INFO] Selected 19 target genomes.
[2024-01-24 12:39:07,289] [INFO] Target genome list was writen to GCF_013409575.1_ASM1340957v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:07,310] [INFO] Task started: fastANI
[2024-01-24 12:39:07,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b55cbbb-571f-4a67-ac29-172b2cb10381/GCF_013409575.1_ASM1340957v1_genomic.fna.gz --refList GCF_013409575.1_ASM1340957v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013409575.1_ASM1340957v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:39:20,626] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:20,638] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:39:20,638] [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_013409575.1	s__Macellibacteroides fermentans	100.0	1298	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Macellibacteroides	95.0	96.90	95.56	0.80	0.74	5	conclusive
GCA_018054455.1	s__Macellibacteroides sp018054455	80.9193	496	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Macellibacteroides	95.0	98.91	97.71	0.78	0.74	5	-
GCF_000156495.1	s__Parabacteroides johnsonii	77.9359	122	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.42	96.67	0.88	0.77	13	-
GCF_000969835.1	s__Parabacteroides goldsteinii	77.9345	165	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.03	95.33	0.85	0.78	37	-
GCF_900128505.1	s__Parabacteroides timonensis	77.8947	167	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.14	96.11	0.85	0.79	3	-
GCF_000969825.1	s__Parabacteroides gordonii	77.8578	174	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.64	96.69	0.92	0.81	6	-
GCF_015550595.1	s__Parabacteroides sp900540715	77.8229	180	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.96	99.96	0.98	0.97	3	-
GCA_900760525.1	s__Parabacteroides sp900760525	77.5171	111	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.93	98.92	0.84	0.82	3	-
GCF_014647375.1	s__Parabacteroides faecis	77.4	172	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.52	97.91	0.91	0.84	9	-
GCF_000187895.1	s__Phocaeicola plebeius	77.1119	55	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.22	96.70	0.79	0.55	12	-
GCF_900128905.1	s__Bacteroides_G luti	76.5088	60	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides_G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:39:20,640] [INFO] GTDB search result was written to GCF_013409575.1_ASM1340957v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:39:20,641] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:39:20,646] [INFO] DFAST_QC result json was written to GCF_013409575.1_ASM1340957v1_genomic.fna/dqc_result.json
[2024-01-24 12:39:20,646] [INFO] DFAST_QC completed!
[2024-01-24 12:39:20,646] [INFO] Total running time: 0h1m43s