[2023-03-16 07:28:29,979] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:28:29,979] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:28:29,979] [INFO] DQC Reference Directory: /var/lib/cwl/stga837a800-da5a-4df3-a319-5c51c8bdd7a2/dqc_reference
[2023-03-16 07:28:31,106] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:28:31,106] [INFO] Task started: Prodigal
[2023-03-16 07:28:31,107] [INFO] Running command: cat /var/lib/cwl/stg2e116fb9-dd28-48c5-a67d-5f1ace9baa5a/OceanDNA-b2842.fa | prodigal -d OceanDNA-b2842/cds.fna -a OceanDNA-b2842/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:29:00,880] [INFO] Task succeeded: Prodigal
[2023-03-16 07:29:00,880] [INFO] Task started: HMMsearch
[2023-03-16 07:29:00,880] [INFO] Running command: hmmsearch --tblout OceanDNA-b2842/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga837a800-da5a-4df3-a319-5c51c8bdd7a2/dqc_reference/reference_markers.hmm OceanDNA-b2842/protein.faa > /dev/null
[2023-03-16 07:29:01,111] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:29:01,111] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2e116fb9-dd28-48c5-a67d-5f1ace9baa5a/OceanDNA-b2842.fa]
[2023-03-16 07:29:01,146] [INFO] Query marker FASTA was written to OceanDNA-b2842/markers.fasta
[2023-03-16 07:29:01,147] [INFO] Task started: Blastn
[2023-03-16 07:29:01,147] [INFO] Running command: blastn -query OceanDNA-b2842/markers.fasta -db /var/lib/cwl/stga837a800-da5a-4df3-a319-5c51c8bdd7a2/dqc_reference/reference_markers.fasta -out OceanDNA-b2842/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:29:02,143] [INFO] Task succeeded: Blastn
[2023-03-16 07:29:02,145] [INFO] Selected 20 target genomes.
[2023-03-16 07:29:02,145] [INFO] Target genome list was writen to OceanDNA-b2842/target_genomes.txt
[2023-03-16 07:29:02,156] [INFO] Task started: fastANI
[2023-03-16 07:29:02,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e116fb9-dd28-48c5-a67d-5f1ace9baa5a/OceanDNA-b2842.fa --refList OceanDNA-b2842/target_genomes.txt --output OceanDNA-b2842/fastani_result.tsv --threads 1
[2023-03-16 07:29:23,440] [INFO] Task succeeded: fastANI
[2023-03-16 07:29:23,440] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga837a800-da5a-4df3-a319-5c51c8bdd7a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:29:23,441] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga837a800-da5a-4df3-a319-5c51c8bdd7a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:29:23,455] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:29:23,455] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:29:23,455] [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 chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	81.9395	1047	1590	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	81.9186	1057	1590	95	below_threshold
Mycolicibacterium vaccae	strain=NBRC 14118	GCA_001552715.1	1810	1810	type	True	81.8182	939	1590	95	below_threshold
Mycolicibacterium chubuense	strain=NCTC10819	GCA_900453455.1	1800	1800	type	True	81.772	1033	1590	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	81.7189	1030	1590	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_001044255.1	1800	1800	type	True	81.6902	1022	1590	95	below_threshold
Mycolicibacterium vaccae	strain=95051	GCA_001655245.1	1810	1810	type	True	81.6637	1017	1590	95	below_threshold
Mycolicibacterium litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	81.0442	910	1590	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	81.0108	908	1590	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	80.8012	899	1590	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	80.7992	908	1590	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	80.7264	913	1590	95	below_threshold
Mycolicibacterium pulveris	strain=JCM 6370	GCA_010725725.1	36813	36813	type	True	80.1922	808	1590	95	below_threshold
Mycolicibacterium chitae	strain=NCTC10485	GCA_900637205.1	1792	1792	type	True	80.1089	760	1590	95	below_threshold
Mycolicibacterium elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	80.0796	792	1590	95	below_threshold
Mycobacterium palauense	strain=CECT 8779	GCA_002592005.1	2034511	2034511	type	True	80.0736	841	1590	95	below_threshold
Mycolicibacterium chitae	strain=JCM 12403	GCA_010727725.1	1792	1792	type	True	80.0647	781	1590	95	below_threshold
Mycolicibacterium thermoresistibile	strain=ATCC 19527	GCA_000234585.2	1797	1797	type	True	79.8118	712	1590	95	below_threshold
Mycolicibacterium thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	79.7939	722	1590	95	below_threshold
Mycolicibacterium insubricum	strain=JCM 16366	GCA_010731615.1	444597	444597	type	True	79.4488	604	1590	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:29:23,587] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2842/tc_result.tsv
[2023-03-16 07:29:23,588] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:29:23,588] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:29:23,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga837a800-da5a-4df3-a319-5c51c8bdd7a2/dqc_reference/checkm_data
[2023-03-16 07:29:23,589] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:29:23,617] [INFO] Task started: CheckM
[2023-03-16 07:29:23,617] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2842/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2842/checkm_input OceanDNA-b2842/checkm_result
[2023-03-16 07:30:38,252] [INFO] Task succeeded: CheckM
[2023-03-16 07:30:38,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 13.89%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 07:30:38,257] [INFO] ===== Completeness check finished =====
[2023-03-16 07:30:38,257] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:30:38,257] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2842/markers.fasta)
[2023-03-16 07:30:38,258] [INFO] Task started: Blastn
[2023-03-16 07:30:38,258] [INFO] Running command: blastn -query OceanDNA-b2842/markers.fasta -db /var/lib/cwl/stga837a800-da5a-4df3-a319-5c51c8bdd7a2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2842/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:30:39,754] [INFO] Task succeeded: Blastn
[2023-03-16 07:30:39,755] [INFO] Selected 15 target genomes.
[2023-03-16 07:30:39,755] [INFO] Target genome list was writen to OceanDNA-b2842/target_genomes_gtdb.txt
[2023-03-16 07:30:40,199] [INFO] Task started: fastANI
[2023-03-16 07:30:40,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e116fb9-dd28-48c5-a67d-5f1ace9baa5a/OceanDNA-b2842.fa --refList OceanDNA-b2842/target_genomes_gtdb.txt --output OceanDNA-b2842/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:30:58,909] [INFO] Task succeeded: fastANI
[2023-03-16 07:30:58,919] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:30:58,919] [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_010728325.1	s__Mycobacterium poriferae	95.2013	1463	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.01	98.01	0.88	0.88	2	conclusive
GCF_017312405.1	s__Mycobacterium sp017312405	94.2183	1424	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCA_000762985.1	s__Mycobacterium rufum_A	82.0963	1033	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612725.1	s__Mycobacterium austroafricanum	82.0431	1069	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_001044235.1	s__Mycobacterium chlorophenolicum	81.9194	1058	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	98.88	97.93	0.94	0.90	4	-
GCF_001552715.1	s__Mycobacterium vaccae	81.7901	943	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.97	1.00	1.00	3	-
GCF_000266905.1	s__Mycobacterium chubuense_A	81.666	1023	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014190915.1	s__Mycobacterium iranicum_B	81.2825	985	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902705885.1	s__Mycobacterium vanbaalenii_A	81.2667	1046	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222675.1	s__Mycobacterium sp005222675	80.9069	994	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722335.1	s__Mycobacterium flavescens_A	80.8302	878	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001583415.1	s__Mycobacterium phlei	80.8042	907	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_004570325.1	s__Mycobacterium sp004570325	80.8006	887	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731615.1	s__Mycobacterium insubricum	79.4367	605	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001668615.1	s__Mycobacterium sp001668615	79.4207	678	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:30:58,919] [INFO] GTDB search result was written to OceanDNA-b2842/result_gtdb.tsv
[2023-03-16 07:30:58,919] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:30:58,921] [INFO] DFAST_QC result json was written to OceanDNA-b2842/dqc_result.json
[2023-03-16 07:30:58,921] [INFO] DFAST_QC completed!
[2023-03-16 07:30:58,921] [INFO] Total running time: 0h2m29s