[2023-03-16 04:24:46,333] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:24:46,333] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:24:46,334] [INFO] DQC Reference Directory: /var/lib/cwl/stg113b6955-6eda-4440-9b3d-13c691aeac26/dqc_reference
[2023-03-16 04:24:48,115] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:24:48,115] [INFO] Task started: Prodigal
[2023-03-16 04:24:48,115] [INFO] Running command: cat /var/lib/cwl/stg82b03e1a-9402-4b9a-bddc-a2353660a1ef/OceanDNA-b1323.fa | prodigal -d OceanDNA-b1323/cds.fna -a OceanDNA-b1323/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:25:01,046] [INFO] Task succeeded: Prodigal
[2023-03-16 04:25:01,047] [INFO] Task started: HMMsearch
[2023-03-16 04:25:01,047] [INFO] Running command: hmmsearch --tblout OceanDNA-b1323/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg113b6955-6eda-4440-9b3d-13c691aeac26/dqc_reference/reference_markers.hmm OceanDNA-b1323/protein.faa > /dev/null
[2023-03-16 04:25:01,233] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:25:01,234] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg82b03e1a-9402-4b9a-bddc-a2353660a1ef/OceanDNA-b1323.fa]
[2023-03-16 04:25:01,249] [INFO] Query marker FASTA was written to OceanDNA-b1323/markers.fasta
[2023-03-16 04:25:01,249] [INFO] Task started: Blastn
[2023-03-16 04:25:01,249] [INFO] Running command: blastn -query OceanDNA-b1323/markers.fasta -db /var/lib/cwl/stg113b6955-6eda-4440-9b3d-13c691aeac26/dqc_reference/reference_markers.fasta -out OceanDNA-b1323/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:25:01,868] [INFO] Task succeeded: Blastn
[2023-03-16 04:25:01,869] [INFO] Selected 28 target genomes.
[2023-03-16 04:25:01,869] [INFO] Target genome list was writen to OceanDNA-b1323/target_genomes.txt
[2023-03-16 04:25:01,883] [INFO] Task started: fastANI
[2023-03-16 04:25:01,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg82b03e1a-9402-4b9a-bddc-a2353660a1ef/OceanDNA-b1323.fa --refList OceanDNA-b1323/target_genomes.txt --output OceanDNA-b1323/fastani_result.tsv --threads 1
[2023-03-16 04:25:22,017] [INFO] Task succeeded: fastANI
[2023-03-16 04:25:22,017] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg113b6955-6eda-4440-9b3d-13c691aeac26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:25:22,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg113b6955-6eda-4440-9b3d-13c691aeac26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:25:22,023] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:25:22,024] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:25:22,024] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.6885	89	669	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.4263	93	669	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.1729	71	669	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.0668	59	669	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.9684	54	669	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	75.4087	53	669	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:25:22,024] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1323/tc_result.tsv
[2023-03-16 04:25:22,024] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:25:22,024] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:25:22,024] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg113b6955-6eda-4440-9b3d-13c691aeac26/dqc_reference/checkm_data
[2023-03-16 04:25:22,025] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:25:22,029] [INFO] Task started: CheckM
[2023-03-16 04:25:22,029] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1323/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1323/checkm_input OceanDNA-b1323/checkm_result
[2023-03-16 04:25:56,959] [INFO] Task succeeded: CheckM
[2023-03-16 04:25:56,959] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 04:25:56,961] [INFO] ===== Completeness check finished =====
[2023-03-16 04:25:56,962] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:25:56,962] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1323/markers.fasta)
[2023-03-16 04:25:56,962] [INFO] Task started: Blastn
[2023-03-16 04:25:56,962] [INFO] Running command: blastn -query OceanDNA-b1323/markers.fasta -db /var/lib/cwl/stg113b6955-6eda-4440-9b3d-13c691aeac26/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1323/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:25:57,897] [INFO] Task succeeded: Blastn
[2023-03-16 04:25:57,898] [INFO] Selected 14 target genomes.
[2023-03-16 04:25:57,898] [INFO] Target genome list was writen to OceanDNA-b1323/target_genomes_gtdb.txt
[2023-03-16 04:25:57,944] [INFO] Task started: fastANI
[2023-03-16 04:25:57,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg82b03e1a-9402-4b9a-bddc-a2353660a1ef/OceanDNA-b1323.fa --refList OceanDNA-b1323/target_genomes_gtdb.txt --output OceanDNA-b1323/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:26:05,107] [INFO] Task succeeded: fastANI
[2023-03-16 04:26:05,114] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:26:05,115] [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_002714485.1	s__UBA9410 sp002714485	98.8806	532	669	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014239855.1	s__UBA9410 sp014239855	81.0675	462	669	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003541675.1	s__UBA9410 sp003541675	80.7882	282	669	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014237715.1	s__UBA9410 sp014237715	80.7871	465	669	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.52	98.52	0.97	0.97	2	-
GCA_016845305.1	s__UBA9410 sp016845305	80.2163	435	669	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002727895.1	s__UBA9410 sp002727895	79.8711	310	669	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	97.12	97.12	0.93	0.93	2	-
GCA_012961035.1	s__UBA9410 sp012961035	78.5579	295	669	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	99.67	99.67	0.93	0.93	2	-
GCA_002346745.1	s__S20-B6 sp002346745	78.5448	234	669	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	97.72	96.97	0.85	0.81	8	-
GCA_014240365.1	s__UBA9410 sp014240365	78.3515	256	669	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.11	98.07	0.86	0.84	5	-
GCA_002699725.1	s__S20-B6 sp002699725	77.5197	203	669	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	98.58	98.41	0.87	0.86	3	-
GCA_014381945.1	s__S20-B6 sp014381945	77.4883	211	669	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002375.1	s__JABDJW01 sp013002375	76.0359	66	669	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SHLQ01;g__JABDJW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:26:05,115] [INFO] GTDB search result was written to OceanDNA-b1323/result_gtdb.tsv
[2023-03-16 04:26:05,115] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:26:05,116] [INFO] DFAST_QC result json was written to OceanDNA-b1323/dqc_result.json
[2023-03-16 04:26:05,116] [INFO] DFAST_QC completed!
[2023-03-16 04:26:05,116] [INFO] Total running time: 0h1m19s