[2023-06-29 11:51:55,110] [INFO] DFAST_QC pipeline started.
[2023-06-29 11:51:55,112] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 11:51:55,112] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ece3753-7bff-4b0f-948d-70fe54303b5e/dqc_reference
[2023-06-29 11:51:56,675] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 11:51:56,676] [INFO] Task started: Prodigal
[2023-06-29 11:51:56,676] [INFO] Running command: gunzip -c /var/lib/cwl/stgb028389e-9c67-43de-99a5-ef5339622dae/GCA_020623865.1_ASM2062386v1_genomic.fna.gz | prodigal -d GCA_020623865.1_ASM2062386v1_genomic.fna/cds.fna -a GCA_020623865.1_ASM2062386v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 11:52:00,669] [INFO] Task succeeded: Prodigal
[2023-06-29 11:52:00,669] [INFO] Task started: HMMsearch
[2023-06-29 11:52:00,669] [INFO] Running command: hmmsearch --tblout GCA_020623865.1_ASM2062386v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ece3753-7bff-4b0f-948d-70fe54303b5e/dqc_reference/reference_markers.hmm GCA_020623865.1_ASM2062386v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 11:52:00,960] [INFO] Task succeeded: HMMsearch
[2023-06-29 11:52:00,961] [INFO] Found 6/6 markers.
[2023-06-29 11:52:00,987] [INFO] Query marker FASTA was written to GCA_020623865.1_ASM2062386v1_genomic.fna/markers.fasta
[2023-06-29 11:52:00,987] [INFO] Task started: Blastn
[2023-06-29 11:52:00,987] [INFO] Running command: blastn -query GCA_020623865.1_ASM2062386v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ece3753-7bff-4b0f-948d-70fe54303b5e/dqc_reference/reference_markers.fasta -out GCA_020623865.1_ASM2062386v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 11:52:01,608] [INFO] Task succeeded: Blastn
[2023-06-29 11:52:01,612] [INFO] Selected 22 target genomes.
[2023-06-29 11:52:01,612] [INFO] Target genome list was writen to GCA_020623865.1_ASM2062386v1_genomic.fna/target_genomes.txt
[2023-06-29 11:52:01,628] [INFO] Task started: fastANI
[2023-06-29 11:52:01,628] [INFO] Running command: fastANI --query /var/lib/cwl/stgb028389e-9c67-43de-99a5-ef5339622dae/GCA_020623865.1_ASM2062386v1_genomic.fna.gz --refList GCA_020623865.1_ASM2062386v1_genomic.fna/target_genomes.txt --output GCA_020623865.1_ASM2062386v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 11:52:14,784] [INFO] Task succeeded: fastANI
[2023-06-29 11:52:14,784] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ece3753-7bff-4b0f-948d-70fe54303b5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 11:52:14,784] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ece3753-7bff-4b0f-948d-70fe54303b5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 11:52:14,789] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2023-06-29 11:52:14,789] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 11:52:14,789] [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
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	95.7434	419	455	95	conclusive
Lachnospira multipara	strain=ATCC 19207	GCA_000424105.1	28051	28051	type	True	78.4492	98	455	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 11:52:14,792] [INFO] DFAST Taxonomy check result was written to GCA_020623865.1_ASM2062386v1_genomic.fna/tc_result.tsv
[2023-06-29 11:52:14,793] [INFO] ===== Taxonomy check completed =====
[2023-06-29 11:52:14,793] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 11:52:14,793] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ece3753-7bff-4b0f-948d-70fe54303b5e/dqc_reference/checkm_data
[2023-06-29 11:52:14,794] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 11:52:14,827] [INFO] Task started: CheckM
[2023-06-29 11:52:14,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020623865.1_ASM2062386v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020623865.1_ASM2062386v1_genomic.fna/checkm_input GCA_020623865.1_ASM2062386v1_genomic.fna/checkm_result
[2023-06-29 11:52:34,894] [INFO] Task succeeded: CheckM
[2023-06-29 11:52:34,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 11:52:34,916] [INFO] ===== Completeness check finished =====
[2023-06-29 11:52:34,917] [INFO] ===== Start GTDB Search =====
[2023-06-29 11:52:34,917] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020623865.1_ASM2062386v1_genomic.fna/markers.fasta)
[2023-06-29 11:52:34,917] [INFO] Task started: Blastn
[2023-06-29 11:52:34,918] [INFO] Running command: blastn -query GCA_020623865.1_ASM2062386v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ece3753-7bff-4b0f-948d-70fe54303b5e/dqc_reference/reference_markers_gtdb.fasta -out GCA_020623865.1_ASM2062386v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 11:52:35,730] [INFO] Task succeeded: Blastn
[2023-06-29 11:52:35,737] [INFO] Selected 10 target genomes.
[2023-06-29 11:52:35,737] [INFO] Target genome list was writen to GCA_020623865.1_ASM2062386v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 11:52:35,747] [INFO] Task started: fastANI
[2023-06-29 11:52:35,747] [INFO] Running command: fastANI --query /var/lib/cwl/stgb028389e-9c67-43de-99a5-ef5339622dae/GCA_020623865.1_ASM2062386v1_genomic.fna.gz --refList GCA_020623865.1_ASM2062386v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020623865.1_ASM2062386v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 11:52:40,537] [INFO] Task succeeded: fastANI
[2023-06-29 11:52:40,551] [INFO] Found 9 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-29 11:52:40,552] [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_009680455.1	s__Lachnospira eligens_A	97.7854	430	455	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.6336	97.83	97.23	0.89	0.81	35	inconclusive
GCF_000146185.1	s__Lachnospira eligens	95.7434	419	455	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.6336	96.66	95.71	0.87	0.85	3	inconclusive
GCF_003464165.1	s__Lachnospira sp003451515	94.5903	403	455	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	97.95	97.44	0.88	0.84	9	-
GCF_003458705.1	s__Lachnospira sp003537285	94.3085	403	455	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.4867	98.01	96.87	0.87	0.80	8	-
GCA_900112995.1	s__Lachnospira rogosae_A	79.5479	190	455	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	99.05	98.51	0.91	0.85	17	-
GCA_900772425.1	s__Lachnospira sp900772425	79.3998	109	455	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000436535.1	s__Lachnospira sp000436535	79.1287	167	455	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.91	98.77	0.95	0.93	6	-
GCA_002435585.1	s__Lachnospira sp002435585	78.6807	150	455	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545725.1	s__Lachnospira sp900545725	78.2585	138	455	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.88	98.45	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2023-06-29 11:52:40,554] [INFO] GTDB search result was written to GCA_020623865.1_ASM2062386v1_genomic.fna/result_gtdb.tsv
[2023-06-29 11:52:40,555] [INFO] ===== GTDB Search completed =====
[2023-06-29 11:52:40,558] [INFO] DFAST_QC result json was written to GCA_020623865.1_ASM2062386v1_genomic.fna/dqc_result.json
[2023-06-29 11:52:40,558] [INFO] DFAST_QC completed!
[2023-06-29 11:52:40,558] [INFO] Total running time: 0h0m45s