[2024-01-24 13:41:25,800] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:25,802] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:25,802] [INFO] DQC Reference Directory: /var/lib/cwl/stgaaae7339-2836-44b9-8475-76e79b99bb8c/dqc_reference
[2024-01-24 13:41:27,171] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:27,172] [INFO] Task started: Prodigal
[2024-01-24 13:41:27,172] [INFO] Running command: gunzip -c /var/lib/cwl/stgf0ae7367-a844-409c-99b7-d2d4615a5f21/GCF_010729305.1_ASM1072930v1_genomic.fna.gz | prodigal -d GCF_010729305.1_ASM1072930v1_genomic.fna/cds.fna -a GCF_010729305.1_ASM1072930v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:49,135] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:49,135] [INFO] Task started: HMMsearch
[2024-01-24 13:41:49,136] [INFO] Running command: hmmsearch --tblout GCF_010729305.1_ASM1072930v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaaae7339-2836-44b9-8475-76e79b99bb8c/dqc_reference/reference_markers.hmm GCF_010729305.1_ASM1072930v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:49,527] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:49,528] [INFO] Found 6/6 markers.
[2024-01-24 13:41:49,579] [INFO] Query marker FASTA was written to GCF_010729305.1_ASM1072930v1_genomic.fna/markers.fasta
[2024-01-24 13:41:49,580] [INFO] Task started: Blastn
[2024-01-24 13:41:49,580] [INFO] Running command: blastn -query GCF_010729305.1_ASM1072930v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaaae7339-2836-44b9-8475-76e79b99bb8c/dqc_reference/reference_markers.fasta -out GCF_010729305.1_ASM1072930v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:50,876] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:50,881] [INFO] Selected 12 target genomes.
[2024-01-24 13:41:50,882] [INFO] Target genome list was writen to GCF_010729305.1_ASM1072930v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:50,892] [INFO] Task started: fastANI
[2024-01-24 13:41:50,892] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0ae7367-a844-409c-99b7-d2d4615a5f21/GCF_010729305.1_ASM1072930v1_genomic.fna.gz --refList GCF_010729305.1_ASM1072930v1_genomic.fna/target_genomes.txt --output GCF_010729305.1_ASM1072930v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:07,655] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:07,656] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaaae7339-2836-44b9-8475-76e79b99bb8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:07,656] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaaae7339-2836-44b9-8475-76e79b99bb8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:07,667] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:42:07,667] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:07,667] [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
Mycolicibacterium psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	100.0	1910	1910	95	conclusive
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	91.4325	1586	1910	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	91.4169	1601	1910	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_001044255.1	1800	1800	type	True	91.1696	1569	1910	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	91.1695	1582	1910	95	below_threshold
Mycolicibacterium chubuense	strain=NCTC10819	GCA_900453455.1	1800	1800	type	True	91.1471	1616	1910	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	81.651	1071	1910	95	below_threshold
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	80.6022	1047	1910	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	80.5971	1037	1910	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	80.1588	858	1910	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	80.1439	912	1910	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	79.7707	812	1910	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:07,669] [INFO] DFAST Taxonomy check result was written to GCF_010729305.1_ASM1072930v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:07,669] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:07,669] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:07,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaaae7339-2836-44b9-8475-76e79b99bb8c/dqc_reference/checkm_data
[2024-01-24 13:42:07,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:07,724] [INFO] Task started: CheckM
[2024-01-24 13:42:07,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010729305.1_ASM1072930v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010729305.1_ASM1072930v1_genomic.fna/checkm_input GCF_010729305.1_ASM1072930v1_genomic.fna/checkm_result
[2024-01-24 13:43:26,059] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:26,061] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:26,080] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:26,081] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:26,081] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010729305.1_ASM1072930v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:26,082] [INFO] Task started: Blastn
[2024-01-24 13:43:26,082] [INFO] Running command: blastn -query GCF_010729305.1_ASM1072930v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaaae7339-2836-44b9-8475-76e79b99bb8c/dqc_reference/reference_markers_gtdb.fasta -out GCF_010729305.1_ASM1072930v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:28,127] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:28,132] [INFO] Selected 10 target genomes.
[2024-01-24 13:43:28,132] [INFO] Target genome list was writen to GCF_010729305.1_ASM1072930v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:28,165] [INFO] Task started: fastANI
[2024-01-24 13:43:28,166] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0ae7367-a844-409c-99b7-d2d4615a5f21/GCF_010729305.1_ASM1072930v1_genomic.fna.gz --refList GCF_010729305.1_ASM1072930v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010729305.1_ASM1072930v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:42,426] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:42,443] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:42,443] [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_010729305.1	s__Mycobacterium psychrotolerans	100.0	1910	1910	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.53	96.53	0.90	0.90	2	conclusive
GCF_001044235.1	s__Mycobacterium chlorophenolicum	91.4123	1589	1910	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	98.88	97.93	0.94	0.90	4	-
GCF_001044255.1	s__Mycobacterium chubuense	91.1822	1567	1910	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	99.98	99.97	0.99	0.98	3	-
GCA_000762985.1	s__Mycobacterium rufum_A	89.1214	1562	1910	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001044245.1	s__Mycobacterium obuense	84.2276	1272	1910	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.74	96.27	0.88	0.86	5	-
GCF_007096635.1	s__Mycobacterium sp007096635	84.132	1240	1910	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000266905.1	s__Mycobacterium chubuense_A	83.1966	1329	1910	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001545925.1	s__Mycobacterium sp001545925	82.944	990	1910	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010723735.1	s__Mycobacterium hippocampi_B	82.0391	1170	1910	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108565.1	s__Mycobacterium rutilum	81.6953	1065	1910	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:42,444] [INFO] GTDB search result was written to GCF_010729305.1_ASM1072930v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:42,445] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:42,448] [INFO] DFAST_QC result json was written to GCF_010729305.1_ASM1072930v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:42,448] [INFO] DFAST_QC completed!
[2024-01-24 13:43:42,448] [INFO] Total running time: 0h2m17s