[2023-06-05 03:28:36,791] [INFO] DFAST_QC pipeline started.
[2023-06-05 03:28:36,793] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 03:28:36,794] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b43e4ca-c226-426c-9bd3-42087232b7f2/dqc_reference
[2023-06-05 03:28:38,012] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 03:28:38,013] [INFO] Task started: Prodigal
[2023-06-05 03:28:38,013] [INFO] Running command: gunzip -c /var/lib/cwl/stg3548eac0-f4eb-4744-84e3-7694672fbe18/GCA_934320905.1_ERR7746048_bin.88_genomic.fna.gz | prodigal -d GCA_934320905.1_ERR7746048_bin.88_genomic.fna/cds.fna -a GCA_934320905.1_ERR7746048_bin.88_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 03:28:43,459] [INFO] Task succeeded: Prodigal
[2023-06-05 03:28:43,459] [INFO] Task started: HMMsearch
[2023-06-05 03:28:43,460] [INFO] Running command: hmmsearch --tblout GCA_934320905.1_ERR7746048_bin.88_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b43e4ca-c226-426c-9bd3-42087232b7f2/dqc_reference/reference_markers.hmm GCA_934320905.1_ERR7746048_bin.88_genomic.fna/protein.faa > /dev/null
[2023-06-05 03:28:43,697] [INFO] Task succeeded: HMMsearch
[2023-06-05 03:28:43,699] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3548eac0-f4eb-4744-84e3-7694672fbe18/GCA_934320905.1_ERR7746048_bin.88_genomic.fna.gz]
[2023-06-05 03:28:43,722] [INFO] Query marker FASTA was written to GCA_934320905.1_ERR7746048_bin.88_genomic.fna/markers.fasta
[2023-06-05 03:28:43,722] [INFO] Task started: Blastn
[2023-06-05 03:28:43,723] [INFO] Running command: blastn -query GCA_934320905.1_ERR7746048_bin.88_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b43e4ca-c226-426c-9bd3-42087232b7f2/dqc_reference/reference_markers.fasta -out GCA_934320905.1_ERR7746048_bin.88_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 03:28:44,320] [INFO] Task succeeded: Blastn
[2023-06-05 03:28:44,324] [INFO] Selected 20 target genomes.
[2023-06-05 03:28:44,325] [INFO] Target genome list was writen to GCA_934320905.1_ERR7746048_bin.88_genomic.fna/target_genomes.txt
[2023-06-05 03:28:44,325] [INFO] Task started: fastANI
[2023-06-05 03:28:44,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg3548eac0-f4eb-4744-84e3-7694672fbe18/GCA_934320905.1_ERR7746048_bin.88_genomic.fna.gz --refList GCA_934320905.1_ERR7746048_bin.88_genomic.fna/target_genomes.txt --output GCA_934320905.1_ERR7746048_bin.88_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 03:28:54,417] [INFO] Task succeeded: fastANI
[2023-06-05 03:28:54,417] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b43e4ca-c226-426c-9bd3-42087232b7f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 03:28:54,418] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b43e4ca-c226-426c-9bd3-42087232b7f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 03:28:54,432] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 03:28:54,432] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 03:28:54,432] [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	79.3418	250	800	95	below_threshold
Lachnospira multipara	strain=ATCC 19207	GCA_000424105.1	28051	28051	type	True	78.4044	116	800	95	below_threshold
Wujia chipingensis	strain=NSJ-4	GCA_014337155.1	2763670	2763670	type	True	77.3026	55	800	95	below_threshold
Butyrivibrio crossotus	strain=DSM 2876	GCA_025148445.1	45851	45851	type	True	77.2516	72	800	95	below_threshold
Butyrivibrio crossotus	strain=DSM 2876	GCA_000156015.1	45851	45851	type	True	77.1832	70	800	95	below_threshold
Eubacterium uniforme	strain=ATCC 35992	GCA_900167115.1	39495	39495	type	True	76.6626	56	800	95	below_threshold
[Clostridium] fimetarium	strain=DSM 9179	GCA_900111235.1	99656	99656	type	True	76.3	56	800	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 03:28:54,434] [INFO] DFAST Taxonomy check result was written to GCA_934320905.1_ERR7746048_bin.88_genomic.fna/tc_result.tsv
[2023-06-05 03:28:54,435] [INFO] ===== Taxonomy check completed =====
[2023-06-05 03:28:54,435] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 03:28:54,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b43e4ca-c226-426c-9bd3-42087232b7f2/dqc_reference/checkm_data
[2023-06-05 03:28:54,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 03:28:54,467] [INFO] Task started: CheckM
[2023-06-05 03:28:54,467] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934320905.1_ERR7746048_bin.88_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934320905.1_ERR7746048_bin.88_genomic.fna/checkm_input GCA_934320905.1_ERR7746048_bin.88_genomic.fna/checkm_result
[2023-06-05 03:29:17,341] [INFO] Task succeeded: CheckM
[2023-06-05 03:29:17,342] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 03:29:17,362] [INFO] ===== Completeness check finished =====
[2023-06-05 03:29:17,362] [INFO] ===== Start GTDB Search =====
[2023-06-05 03:29:17,363] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934320905.1_ERR7746048_bin.88_genomic.fna/markers.fasta)
[2023-06-05 03:29:17,363] [INFO] Task started: Blastn
[2023-06-05 03:29:17,363] [INFO] Running command: blastn -query GCA_934320905.1_ERR7746048_bin.88_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b43e4ca-c226-426c-9bd3-42087232b7f2/dqc_reference/reference_markers_gtdb.fasta -out GCA_934320905.1_ERR7746048_bin.88_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 03:29:18,245] [INFO] Task succeeded: Blastn
[2023-06-05 03:29:18,264] [INFO] Selected 14 target genomes.
[2023-06-05 03:29:18,265] [INFO] Target genome list was writen to GCA_934320905.1_ERR7746048_bin.88_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 03:29:18,267] [INFO] Task started: fastANI
[2023-06-05 03:29:18,267] [INFO] Running command: fastANI --query /var/lib/cwl/stg3548eac0-f4eb-4744-84e3-7694672fbe18/GCA_934320905.1_ERR7746048_bin.88_genomic.fna.gz --refList GCA_934320905.1_ERR7746048_bin.88_genomic.fna/target_genomes_gtdb.txt --output GCA_934320905.1_ERR7746048_bin.88_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 03:29:24,645] [INFO] Task succeeded: fastANI
[2023-06-05 03:29:24,659] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 03:29:24,660] [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_900547255.1	s__Lachnospira sp900547255	98.2924	615	800	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	99.87	99.87	0.91	0.91	2	conclusive
GCF_000146185.1	s__Lachnospira eligens	79.3615	249	800	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.6336	96.66	95.71	0.87	0.85	3	-
GCF_003458705.1	s__Lachnospira sp003537285	79.3038	255	800	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.4867	98.01	96.87	0.87	0.80	8	-
GCF_009680455.1	s__Lachnospira eligens_A	79.2786	255	800	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.6336	97.83	97.23	0.89	0.81	35	-
GCF_003464165.1	s__Lachnospira sp003451515	79.26	232	800	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_014287955.1	s__Lachnospira sp900316325	79.2436	251	800	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.86	98.35	0.93	0.88	10	-
GCA_900112995.1	s__Lachnospira rogosae_A	79.1566	249	800	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_000436535.1	s__Lachnospira sp000436535	78.6817	233	800	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_000436475.1	s__Lachnospira sp000436475	78.4743	238	800	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	97.97	97.42	0.90	0.86	10	-
GCA_002435585.1	s__Lachnospira sp002435585	78.2598	185	800	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	78.2576	201	800	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.88	98.45	0.88	0.87	3	-
GCA_002394205.1	s__Lachnospira sp002394205	77.7115	116	800	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	99.96	99.94	0.94	0.91	3	-
GCA_910589305.1	s__Lachnospira sp910589305	77.5281	100	800	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_910587485.1	s__Lachnospira sp910587485	77.1277	114	800	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 03:29:24,679] [INFO] GTDB search result was written to GCA_934320905.1_ERR7746048_bin.88_genomic.fna/result_gtdb.tsv
[2023-06-05 03:29:24,680] [INFO] ===== GTDB Search completed =====
[2023-06-05 03:29:24,690] [INFO] DFAST_QC result json was written to GCA_934320905.1_ERR7746048_bin.88_genomic.fna/dqc_result.json
[2023-06-05 03:29:24,691] [INFO] DFAST_QC completed!
[2023-06-05 03:29:24,691] [INFO] Total running time: 0h0m48s