[2023-03-18 07:29:32,024] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:32,024] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:32,024] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f2b2f55-ffe8-4cd0-b721-6b4206322d63/dqc_reference
[2023-03-18 07:29:33,110] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:33,110] [INFO] Task started: Prodigal
[2023-03-18 07:29:33,110] [INFO] Running command: cat /var/lib/cwl/stg490e1aa3-bbe6-49d5-9469-7bc22f91cf07/OceanDNA-b23040.fa | prodigal -d OceanDNA-b23040/cds.fna -a OceanDNA-b23040/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:48,287] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:48,288] [INFO] Task started: HMMsearch
[2023-03-18 07:29:48,288] [INFO] Running command: hmmsearch --tblout OceanDNA-b23040/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f2b2f55-ffe8-4cd0-b721-6b4206322d63/dqc_reference/reference_markers.hmm OceanDNA-b23040/protein.faa > /dev/null
[2023-03-18 07:29:48,446] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:48,446] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg490e1aa3-bbe6-49d5-9469-7bc22f91cf07/OceanDNA-b23040.fa]
[2023-03-18 07:29:48,461] [INFO] Query marker FASTA was written to OceanDNA-b23040/markers.fasta
[2023-03-18 07:29:48,461] [INFO] Task started: Blastn
[2023-03-18 07:29:48,461] [INFO] Running command: blastn -query OceanDNA-b23040/markers.fasta -db /var/lib/cwl/stg6f2b2f55-ffe8-4cd0-b721-6b4206322d63/dqc_reference/reference_markers.fasta -out OceanDNA-b23040/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:49,021] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:49,022] [INFO] Selected 17 target genomes.
[2023-03-18 07:29:49,022] [INFO] Target genome list was writen to OceanDNA-b23040/target_genomes.txt
[2023-03-18 07:29:49,031] [INFO] Task started: fastANI
[2023-03-18 07:29:49,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg490e1aa3-bbe6-49d5-9469-7bc22f91cf07/OceanDNA-b23040.fa --refList OceanDNA-b23040/target_genomes.txt --output OceanDNA-b23040/fastani_result.tsv --threads 1
[2023-03-18 07:30:02,887] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:02,887] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f2b2f55-ffe8-4cd0-b721-6b4206322d63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:30:02,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f2b2f55-ffe8-4cd0-b721-6b4206322d63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:30:02,894] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:30:02,894] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:30:02,894] [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
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	74.8828	70	639	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	74.855	63	639	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	74.8523	64	639	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	74.8414	65	639	95	below_threshold
Salinarimonas ramus	strain=CGMCC 1.9161	GCA_014645695.1	690164	690164	type	True	74.7891	71	639	95	below_threshold
Actinomadura mexicana	strain=DSM 44485	GCA_900188105.1	134959	134959	type	True	74.7875	119	639	95	below_threshold
Actinomadura citrea	strain=DSM 43461	GCA_013409045.1	46158	46158	type	True	74.7702	117	639	95	below_threshold
Actinomadura citrea	strain=JCM 3295	GCA_014648455.1	46158	46158	type	True	74.7662	119	639	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.6923	106	639	95	below_threshold
Amycolatopsis circi	strain=DSM 45561	GCA_003385235.1	871959	871959	type	True	74.6657	63	639	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:30:02,894] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23040/tc_result.tsv
[2023-03-18 07:30:02,894] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:30:02,895] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:30:02,895] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f2b2f55-ffe8-4cd0-b721-6b4206322d63/dqc_reference/checkm_data
[2023-03-18 07:30:02,895] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:30:02,899] [INFO] Task started: CheckM
[2023-03-18 07:30:02,899] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23040/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23040/checkm_input OceanDNA-b23040/checkm_result
[2023-03-18 07:30:42,114] [INFO] Task succeeded: CheckM
[2023-03-18 07:30:42,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.31%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:30:42,116] [INFO] ===== Completeness check finished =====
[2023-03-18 07:30:42,117] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:30:42,117] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23040/markers.fasta)
[2023-03-18 07:30:42,117] [INFO] Task started: Blastn
[2023-03-18 07:30:42,117] [INFO] Running command: blastn -query OceanDNA-b23040/markers.fasta -db /var/lib/cwl/stg6f2b2f55-ffe8-4cd0-b721-6b4206322d63/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23040/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:30:42,924] [INFO] Task succeeded: Blastn
[2023-03-18 07:30:42,924] [INFO] Selected 8 target genomes.
[2023-03-18 07:30:42,924] [INFO] Target genome list was writen to OceanDNA-b23040/target_genomes_gtdb.txt
[2023-03-18 07:30:43,122] [INFO] Task started: fastANI
[2023-03-18 07:30:43,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg490e1aa3-bbe6-49d5-9469-7bc22f91cf07/OceanDNA-b23040.fa --refList OceanDNA-b23040/target_genomes_gtdb.txt --output OceanDNA-b23040/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:30:49,405] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:49,410] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:30:49,410] [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	82.1748	514	639	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	81.0014	459	639	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	78.8081	308	639	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	77.7813	271	639	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	76.9026	152	639	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_016779225.1	s__GCA-2686945 sp016779225	76.7508	136	639	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	75.934	107	639	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	-
--------------------------------------------------------------------------------
[2023-03-18 07:30:49,410] [INFO] GTDB search result was written to OceanDNA-b23040/result_gtdb.tsv
[2023-03-18 07:30:49,410] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:30:49,411] [INFO] DFAST_QC result json was written to OceanDNA-b23040/dqc_result.json
[2023-03-18 07:30:49,411] [INFO] DFAST_QC completed!
[2023-03-18 07:30:49,411] [INFO] Total running time: 0h1m17s