[2024-01-24 15:26:39,600] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:39,602] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:39,602] [INFO] DQC Reference Directory: /var/lib/cwl/stg39f4a244-8163-4a97-868c-d5b596043cb7/dqc_reference
[2024-01-24 15:26:40,937] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:40,938] [INFO] Task started: Prodigal
[2024-01-24 15:26:40,939] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa6aee38-1fb4-4f0a-8fae-f07f9864e9f6/GCF_014287775.1_ASM1428777v1_genomic.fna.gz | prodigal -d GCF_014287775.1_ASM1428777v1_genomic.fna/cds.fna -a GCF_014287775.1_ASM1428777v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:46,942] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:46,943] [INFO] Task started: HMMsearch
[2024-01-24 15:26:46,943] [INFO] Running command: hmmsearch --tblout GCF_014287775.1_ASM1428777v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39f4a244-8163-4a97-868c-d5b596043cb7/dqc_reference/reference_markers.hmm GCF_014287775.1_ASM1428777v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:47,230] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:47,231] [INFO] Found 6/6 markers.
[2024-01-24 15:26:47,259] [INFO] Query marker FASTA was written to GCF_014287775.1_ASM1428777v1_genomic.fna/markers.fasta
[2024-01-24 15:26:47,259] [INFO] Task started: Blastn
[2024-01-24 15:26:47,259] [INFO] Running command: blastn -query GCF_014287775.1_ASM1428777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39f4a244-8163-4a97-868c-d5b596043cb7/dqc_reference/reference_markers.fasta -out GCF_014287775.1_ASM1428777v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:47,925] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:47,928] [INFO] Selected 28 target genomes.
[2024-01-24 15:26:47,928] [INFO] Target genome list was writen to GCF_014287775.1_ASM1428777v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:48,253] [INFO] Task started: fastANI
[2024-01-24 15:26:48,254] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa6aee38-1fb4-4f0a-8fae-f07f9864e9f6/GCF_014287775.1_ASM1428777v1_genomic.fna.gz --refList GCF_014287775.1_ASM1428777v1_genomic.fna/target_genomes.txt --output GCF_014287775.1_ASM1428777v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:03,615] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:03,615] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39f4a244-8163-4a97-868c-d5b596043cb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:03,616] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39f4a244-8163-4a97-868c-d5b596043cb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:03,625] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:27:03,625] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:27:03,625] [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
Jutongia hominis	strain=BX3	GCA_014384965.1	2763664	2763664	type	True	82.5468	66	969	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_025150745.1	39496	39496	suspected-type	True	80.7291	305	969	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_000153885.1	39496	39496	suspected-type	True	80.6933	300	969	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	79.2447	51	969	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	79.2421	51	969	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_000156675.1	1322	1322	type	True	79.0649	53	969	95	below_threshold
Velocimicrobium porci	strain=WCA-693-APC-MOT-I	GCA_009696045.1	2606634	2606634	type	True	78.1971	54	969	95	below_threshold
Lachnobacterium bovis	strain=DSM 14045	GCA_900107245.1	140626	140626	suspected-type	True	77.3293	50	969	95	below_threshold
Pseudobutyrivibrio xylanivorans	strain=DSM 14809	GCA_900141825.1	185007	185007	type	True	76.538	54	969	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:03,627] [INFO] DFAST Taxonomy check result was written to GCF_014287775.1_ASM1428777v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:03,627] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:03,628] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:03,628] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39f4a244-8163-4a97-868c-d5b596043cb7/dqc_reference/checkm_data
[2024-01-24 15:27:03,629] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:03,663] [INFO] Task started: CheckM
[2024-01-24 15:27:03,663] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014287775.1_ASM1428777v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014287775.1_ASM1428777v1_genomic.fna/checkm_input GCF_014287775.1_ASM1428777v1_genomic.fna/checkm_result
[2024-01-24 15:27:28,843] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:28,844] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:28,865] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:28,865] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:28,866] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014287775.1_ASM1428777v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:28,866] [INFO] Task started: Blastn
[2024-01-24 15:27:28,866] [INFO] Running command: blastn -query GCF_014287775.1_ASM1428777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39f4a244-8163-4a97-868c-d5b596043cb7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014287775.1_ASM1428777v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:29,891] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:29,902] [INFO] Selected 15 target genomes.
[2024-01-24 15:27:29,902] [INFO] Target genome list was writen to GCF_014287775.1_ASM1428777v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:29,914] [INFO] Task started: fastANI
[2024-01-24 15:27:29,914] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa6aee38-1fb4-4f0a-8fae-f07f9864e9f6/GCF_014287775.1_ASM1428777v1_genomic.fna.gz --refList GCF_014287775.1_ASM1428777v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014287775.1_ASM1428777v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:37,589] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:37,605] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:37,605] [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_003479405.1	s__Eubacterium_G sp000432355	99.2051	833	969	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	99.22	97.56	0.94	0.86	9	conclusive
GCF_000153885.1	s__Eubacterium_G ventriosum	80.6871	301	969	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.27	97.67	0.81	0.64	20	-
GCA_900548465.1	s__Eubacterium_G sp900548465	80.2231	322	969	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	97.75	97.64	0.80	0.72	3	-
GCF_003460505.1	s__Eubacterium_G sp000435815	80.0715	299	969	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.79	97.65	0.84	0.54	8	-
GCA_900550135.1	s__Eubacterium_G sp900550135	79.8918	257	969	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.87	97.32	0.76	0.74	4	-
GCA_902363805.1	s__Eubacterium_G sp000434315	79.4739	230	969	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.27	98.14	0.87	0.84	6	-
GCA_900764695.1	s__Eubacterium_G sp900764695	79.1714	217	969	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910574895.1	s__Eubacterium_G sp910574895	79.0823	227	969	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578975.1	s__Eubacterium_G sp910578975	78.8075	207	969	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584795.1	s__Eubacterium_G sp910584795	78.7912	221	969	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904420085.1	s__Eubacterium_G sp904420085	78.0593	183	969	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017965495.1	s__Eubacterium_G sp017965495	77.8218	58	969	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:37,607] [INFO] GTDB search result was written to GCF_014287775.1_ASM1428777v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:37,608] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:37,611] [INFO] DFAST_QC result json was written to GCF_014287775.1_ASM1428777v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:37,611] [INFO] DFAST_QC completed!
[2024-01-24 15:27:37,611] [INFO] Total running time: 0h0m58s