[2023-03-15 08:59:47,109] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:59:47,110] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:59:47,110] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa7ade31-44bd-4aea-8756-6366375d9e27/dqc_reference
[2023-03-15 08:59:48,228] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:59:48,229] [INFO] Task started: Prodigal
[2023-03-15 08:59:48,229] [INFO] Running command: cat /var/lib/cwl/stgb98fd8ec-3e21-40c3-8164-cf94d7cb52d5/OceanDNA-b23041.fa | prodigal -d OceanDNA-b23041/cds.fna -a OceanDNA-b23041/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:00:12,410] [INFO] Task succeeded: Prodigal
[2023-03-15 09:00:12,410] [INFO] Task started: HMMsearch
[2023-03-15 09:00:12,410] [INFO] Running command: hmmsearch --tblout OceanDNA-b23041/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa7ade31-44bd-4aea-8756-6366375d9e27/dqc_reference/reference_markers.hmm OceanDNA-b23041/protein.faa > /dev/null
[2023-03-15 09:00:12,597] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:00:12,597] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb98fd8ec-3e21-40c3-8164-cf94d7cb52d5/OceanDNA-b23041.fa]
[2023-03-15 09:00:12,622] [INFO] Query marker FASTA was written to OceanDNA-b23041/markers.fasta
[2023-03-15 09:00:12,623] [INFO] Task started: Blastn
[2023-03-15 09:00:12,623] [INFO] Running command: blastn -query OceanDNA-b23041/markers.fasta -db /var/lib/cwl/stgaa7ade31-44bd-4aea-8756-6366375d9e27/dqc_reference/reference_markers.fasta -out OceanDNA-b23041/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:00:13,251] [INFO] Task succeeded: Blastn
[2023-03-15 09:00:13,251] [INFO] Selected 20 target genomes.
[2023-03-15 09:00:13,252] [INFO] Target genome list was writen to OceanDNA-b23041/target_genomes.txt
[2023-03-15 09:00:13,364] [INFO] Task started: fastANI
[2023-03-15 09:00:13,364] [INFO] Running command: fastANI --query /var/lib/cwl/stgb98fd8ec-3e21-40c3-8164-cf94d7cb52d5/OceanDNA-b23041.fa --refList OceanDNA-b23041/target_genomes.txt --output OceanDNA-b23041/fastani_result.tsv --threads 1
[2023-03-15 09:00:31,968] [INFO] Task succeeded: fastANI
[2023-03-15 09:00:31,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa7ade31-44bd-4aea-8756-6366375d9e27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:00:31,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa7ade31-44bd-4aea-8756-6366375d9e27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:00:31,979] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:00:31,979] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 09:00:31,979] [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
Actinomyces viscosus	strain=CCUG 14476	GCA_004525795.1	1656	1656	type	True	74.8361	57	915	95	below_threshold
Actinomyces viscosus	strain=NCTC10951	GCA_900637975.1	1656	1656	type	True	74.8296	58	915	95	below_threshold
Microvirga thermotolerans	strain=HR1	GCA_009363855.1	2651334	2651334	type	True	74.7628	61	915	95	below_threshold
Amycolatopsis rifamycinica	strain=DSM 46095	GCA_000695625.1	287986	287986	type	True	74.7585	143	915	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	74.704	155	915	95	below_threshold
Actinomadura namibiensis	strain=DSM 44197	GCA_014138665.1	182080	182080	type	True	74.6747	212	915	95	below_threshold
Methylobacterium ajmalii	strain=IF7SW-B2	GCA_016613415.1	2738439	2738439	type	True	74.6728	140	915	95	below_threshold
Amycolatopsis mediterranei	strain=S699	GCA_000220945.1	33910	33910	type	True	74.6696	158	915	95	below_threshold
Saccharomonospora iraqiensis subsp. paurometabolica	strain=YIM 90007	GCA_000231035.3	208085	52698	type	True	74.6649	70	915	95	below_threshold
Amycolatopsis vancoresmycina	strain=NRRL B-24208	GCA_000716785.1	208444	208444	type	True	74.6607	144	915	95	below_threshold
Methylobacterium indicum	strain=SE2.11	GCA_001043895.1	1775910	1775910	type	True	74.6594	114	915	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	74.6566	153	915	95	below_threshold
Nocardiopsis aegyptia	strain=DSM 44442	GCA_013410755.1	220378	220378	type	True	74.6494	135	915	95	below_threshold
Amycolatopsis balhimycina	strain=DSM 44591	GCA_000384295.1	208443	208443	type	True	74.6353	135	915	95	below_threshold
Amycolatopsis vancoresmycina	strain=DSM 44592	GCA_000388135.1	208444	208444	type	True	74.6317	121	915	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	74.6145	144	915	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	74.5984	60	915	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	74.5961	99	915	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 09:00:31,980] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23041/tc_result.tsv
[2023-03-15 09:00:31,980] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:00:31,980] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:00:31,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa7ade31-44bd-4aea-8756-6366375d9e27/dqc_reference/checkm_data
[2023-03-15 09:00:31,981] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:00:31,989] [INFO] Task started: CheckM
[2023-03-15 09:00:31,989] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23041/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23041/checkm_input OceanDNA-b23041/checkm_result
[2023-03-15 09:01:30,241] [INFO] Task succeeded: CheckM
[2023-03-15 09:01:30,241] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.29%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:01:30,244] [INFO] ===== Completeness check finished =====
[2023-03-15 09:01:30,244] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:01:30,244] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23041/markers.fasta)
[2023-03-15 09:01:30,244] [INFO] Task started: Blastn
[2023-03-15 09:01:30,244] [INFO] Running command: blastn -query OceanDNA-b23041/markers.fasta -db /var/lib/cwl/stgaa7ade31-44bd-4aea-8756-6366375d9e27/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23041/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:01:31,178] [INFO] Task succeeded: Blastn
[2023-03-15 09:01:31,179] [INFO] Selected 10 target genomes.
[2023-03-15 09:01:31,179] [INFO] Target genome list was writen to OceanDNA-b23041/target_genomes_gtdb.txt
[2023-03-15 09:01:31,216] [INFO] Task started: fastANI
[2023-03-15 09:01:31,216] [INFO] Running command: fastANI --query /var/lib/cwl/stgb98fd8ec-3e21-40c3-8164-cf94d7cb52d5/OceanDNA-b23041.fa --refList OceanDNA-b23041/target_genomes_gtdb.txt --output OceanDNA-b23041/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:01:38,958] [INFO] Task succeeded: fastANI
[2023-03-15 09:01:38,964] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:01:38,964] [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_016779205.1	s__GCA-2862085 sp016779205	82.4576	745	915	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480285.1	s__GCA-2862085 sp905480285	81.1787	658	915	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862085.1	s__GCA-2862085 sp002862085	78.3835	436	915	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007751475.1	s__GCA-2862085 sp007751475	77.762	361	915	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524785.1	s__GCA-2686945 sp011524785	76.7318	187	915	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2686945	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903892045.1	s__F1-120-MAGs118 sp903892045	75.9503	147	915	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	99.41	99.41	0.87	0.87	3	-
GCA_002686265.1	s__GCA-2686265 sp002686265	75.9167	150	915	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2686265	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795205.1	s__JAEUHZ01 sp016795205	75.6943	175	915	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JAEUHZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003566475.1	s__PXDE01 sp003566475	74.7673	56	915	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__SS1-B-03-39;f__PXDE01;g__PXDE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 09:01:38,964] [INFO] GTDB search result was written to OceanDNA-b23041/result_gtdb.tsv
[2023-03-15 09:01:38,965] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:01:38,966] [INFO] DFAST_QC result json was written to OceanDNA-b23041/dqc_result.json
[2023-03-15 09:01:38,966] [INFO] DFAST_QC completed!
[2023-03-15 09:01:38,966] [INFO] Total running time: 0h1m52s