[2023-03-14 11:17:29,595] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:17:29,595] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:17:29,595] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bd8d102-4517-47f1-afc6-ff2f9e2b86c0/dqc_reference
[2023-03-14 11:17:30,709] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:17:30,710] [INFO] Task started: Prodigal
[2023-03-14 11:17:30,710] [INFO] Running command: cat /var/lib/cwl/stg481ff747-6d53-4358-85e8-8791c25ece94/OceanDNA-b2854.fa | prodigal -d OceanDNA-b2854/cds.fna -a OceanDNA-b2854/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:17:55,967] [INFO] Task succeeded: Prodigal
[2023-03-14 11:17:55,967] [INFO] Task started: HMMsearch
[2023-03-14 11:17:55,967] [INFO] Running command: hmmsearch --tblout OceanDNA-b2854/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bd8d102-4517-47f1-afc6-ff2f9e2b86c0/dqc_reference/reference_markers.hmm OceanDNA-b2854/protein.faa > /dev/null
[2023-03-14 11:17:56,176] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:17:56,176] [INFO] Found 6/6 markers.
[2023-03-14 11:17:56,202] [INFO] Query marker FASTA was written to OceanDNA-b2854/markers.fasta
[2023-03-14 11:17:56,203] [INFO] Task started: Blastn
[2023-03-14 11:17:56,203] [INFO] Running command: blastn -query OceanDNA-b2854/markers.fasta -db /var/lib/cwl/stg5bd8d102-4517-47f1-afc6-ff2f9e2b86c0/dqc_reference/reference_markers.fasta -out OceanDNA-b2854/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:17:57,132] [INFO] Task succeeded: Blastn
[2023-03-14 11:17:57,133] [INFO] Selected 27 target genomes.
[2023-03-14 11:17:57,133] [INFO] Target genome list was writen to OceanDNA-b2854/target_genomes.txt
[2023-03-14 11:17:57,150] [INFO] Task started: fastANI
[2023-03-14 11:17:57,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg481ff747-6d53-4358-85e8-8791c25ece94/OceanDNA-b2854.fa --refList OceanDNA-b2854/target_genomes.txt --output OceanDNA-b2854/fastani_result.tsv --threads 1
[2023-03-14 11:18:23,559] [INFO] Task succeeded: fastANI
[2023-03-14 11:18:23,559] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bd8d102-4517-47f1-afc6-ff2f9e2b86c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:18:23,560] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bd8d102-4517-47f1-afc6-ff2f9e2b86c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:18:23,574] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:18:23,574] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:18:23,574] [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=DSM 43826	GCA_001044235.1	37916	37916	type	True	80.1399	779	1329	95	below_threshold
Mycolicibacterium psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	80.1256	755	1329	95	below_threshold
Mycolicibacterium vaccae	strain=95051	GCA_001655245.1	1810	1810	type	True	80.1211	764	1329	95	below_threshold
Mycolicibacterium vaccae	strain=NBRC 14118	GCA_001552715.1	1810	1810	type	True	80.1162	704	1329	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	80.0953	779	1329	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	80.0527	760	1329	95	below_threshold
Mycolicibacterium chubuense	strain=NCTC10819	GCA_900453455.1	1800	1800	type	True	80.0272	775	1329	95	below_threshold
Mycolicibacterium aurum	strain=NCTC10437	GCA_900637195.1	1791	1791	type	True	80.0248	752	1329	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_001044255.1	1800	1800	type	True	80.0027	759	1329	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	79.5828	633	1329	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	79.5036	660	1329	95	below_threshold
Mycolicibacterium chitae	strain=JCM 12403	GCA_010727725.1	1792	1792	type	True	79.0966	563	1329	95	below_threshold
Mycolicibacterium chitae	strain=NCTC10485	GCA_900637205.1	1792	1792	type	True	79.031	565	1329	95	below_threshold
Mycobacterium lehmannii	strain=CECT 8763	GCA_002245535.1	2048550	2048550	type	True	78.9886	578	1329	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	78.9784	581	1329	95	below_threshold
Mycolicibacterium septicum	strain=type strain: DSM 44393	GCA_000455325.1	98668	98668	type	True	78.8649	582	1329	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	78.839	583	1329	95	below_threshold
Mycolicibacterium septicum	strain=ATCC 700731	GCA_012396425.1	98668	98668	type	True	78.8354	585	1329	95	below_threshold
Mycolicibacterium canariasense	strain=JCM15298	GCA_001570445.1	228230	228230	type	True	78.7848	552	1329	95	below_threshold
Mycolicibacterium canariasense	strain=CCUG 47953	GCA_002101555.1	228230	228230	type	True	78.7822	546	1329	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	78.7459	561	1329	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	78.7262	563	1329	95	below_threshold
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	78.7189	595	1329	95	below_threshold
Candidatus Mycolicibacterium alkanivorans		GCA_022760805.1	2954114	2954114	type	True	78.6523	472	1329	95	below_threshold
Mycolicibacterium thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	78.6518	518	1329	95	below_threshold
Mycolicibacterium mengxianglii	strain=Z-34	GCA_015710575.2	2736649	2736649	type	True	78.4496	472	1329	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	78.4424	530	1329	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:18:23,574] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2854/tc_result.tsv
[2023-03-14 11:18:23,574] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:18:23,574] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:18:23,574] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bd8d102-4517-47f1-afc6-ff2f9e2b86c0/dqc_reference/checkm_data
[2023-03-14 11:18:23,575] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:18:23,581] [INFO] Task started: CheckM
[2023-03-14 11:18:23,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2854/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2854/checkm_input OceanDNA-b2854/checkm_result
[2023-03-14 11:19:25,322] [INFO] Task succeeded: CheckM
[2023-03-14 11:19:25,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:19:25,325] [INFO] ===== Completeness check finished =====
[2023-03-14 11:19:25,325] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:19:25,325] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2854/markers.fasta)
[2023-03-14 11:19:25,326] [INFO] Task started: Blastn
[2023-03-14 11:19:25,326] [INFO] Running command: blastn -query OceanDNA-b2854/markers.fasta -db /var/lib/cwl/stg5bd8d102-4517-47f1-afc6-ff2f9e2b86c0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2854/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:19:26,646] [INFO] Task succeeded: Blastn
[2023-03-14 11:19:26,646] [INFO] Selected 23 target genomes.
[2023-03-14 11:19:26,646] [INFO] Target genome list was writen to OceanDNA-b2854/target_genomes_gtdb.txt
[2023-03-14 11:19:26,693] [INFO] Task started: fastANI
[2023-03-14 11:19:26,693] [INFO] Running command: fastANI --query /var/lib/cwl/stg481ff747-6d53-4358-85e8-8791c25ece94/OceanDNA-b2854.fa --refList OceanDNA-b2854/target_genomes_gtdb.txt --output OceanDNA-b2854/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:19:50,131] [INFO] Task succeeded: fastANI
[2023-03-14 11:19:50,144] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:19:50,144] [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_013390125.1	s__Mycobacterium hippocampi_A	82.02	887	1329	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	81.8499	905	1329	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	81.8271	878	1329	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	81.727	892	1329	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	80.4161	767	1329	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	80.3431	814	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_001545925.1	s__Mycobacterium sp001545925	80.2938	657	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000762985.1	s__Mycobacterium rufum_A	80.1438	770	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552715.1	s__Mycobacterium vaccae	80.131	703	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.97	1.00	1.00	3	-
GCF_001044255.1	s__Mycobacterium chubuense	80.0255	755	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	99.98	99.97	0.99	0.98	3	-
GCF_010726645.1	s__Mycobacterium duvalii	79.6433	708	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001722335.1	s__Mycobacterium flavescens_A	79.4081	653	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499995.1	s__Mycobacterium sp001499995	78.9824	603	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101555.1	s__Mycobacterium canariasense	78.7802	545	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000620625.1	s__Mycobacterium sp000620625	78.78	591	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731815.2	s__Mycobacterium arabiense	78.7431	591	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727475.1	s__Mycobacterium mageritense	78.723	564	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.33	0.91	0.85	5	-
GCF_000328565.1	s__Mycobacterium sp000328565	78.6548	567	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853185.1	s__Mycobacterium sp017853185	78.4312	394	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884065.1	s__Mycobacterium sp903884065	78.1074	439	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.70	0.92	0.92	2	-
GCA_903877095.1	s__Mycobacterium sp903877095	78.0842	430	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.96	99.94	0.97	0.96	4	-
GCA_903862565.1	s__Mycobacterium sp903862565	78.0525	406	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005787665.1	s__Mycobacterium sp005787665	77.228	266	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:19:50,144] [INFO] GTDB search result was written to OceanDNA-b2854/result_gtdb.tsv
[2023-03-14 11:19:50,145] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:19:50,147] [INFO] DFAST_QC result json was written to OceanDNA-b2854/dqc_result.json
[2023-03-14 11:19:50,147] [INFO] DFAST_QC completed!
[2023-03-14 11:19:50,147] [INFO] Total running time: 0h2m21s