[2023-03-15 21:01:44,348] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:01:44,348] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:01:44,348] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b774387-2702-41e3-9ec6-1ebbb322cf34/dqc_reference
[2023-03-15 21:01:45,701] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:01:45,701] [INFO] Task started: Prodigal
[2023-03-15 21:01:45,701] [INFO] Running command: cat /var/lib/cwl/stg5c13585d-c552-4064-b9d4-c48df5e7f82a/OceanDNA-b6772.fa | prodigal -d OceanDNA-b6772/cds.fna -a OceanDNA-b6772/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:02:11,898] [INFO] Task succeeded: Prodigal
[2023-03-15 21:02:11,898] [INFO] Task started: HMMsearch
[2023-03-15 21:02:11,898] [INFO] Running command: hmmsearch --tblout OceanDNA-b6772/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b774387-2702-41e3-9ec6-1ebbb322cf34/dqc_reference/reference_markers.hmm OceanDNA-b6772/protein.faa > /dev/null
[2023-03-15 21:02:12,098] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:02:12,099] [INFO] Found 6/6 markers.
[2023-03-15 21:02:12,122] [INFO] Query marker FASTA was written to OceanDNA-b6772/markers.fasta
[2023-03-15 21:02:12,122] [INFO] Task started: Blastn
[2023-03-15 21:02:12,122] [INFO] Running command: blastn -query OceanDNA-b6772/markers.fasta -db /var/lib/cwl/stg5b774387-2702-41e3-9ec6-1ebbb322cf34/dqc_reference/reference_markers.fasta -out OceanDNA-b6772/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:12,757] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:12,758] [INFO] Selected 18 target genomes.
[2023-03-15 21:02:12,759] [INFO] Target genome list was writen to OceanDNA-b6772/target_genomes.txt
[2023-03-15 21:02:12,768] [INFO] Task started: fastANI
[2023-03-15 21:02:12,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c13585d-c552-4064-b9d4-c48df5e7f82a/OceanDNA-b6772.fa --refList OceanDNA-b6772/target_genomes.txt --output OceanDNA-b6772/fastani_result.tsv --threads 1
[2023-03-15 21:02:27,761] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:27,762] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b774387-2702-41e3-9ec6-1ebbb322cf34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:02:27,762] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b774387-2702-41e3-9ec6-1ebbb322cf34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:02:27,772] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:02:27,772] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:02:27,772] [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
Flavobacterium gillisiae	strain=DSM 22376	GCA_900107635.1	150146	150146	type	True	93.5485	1107	1336	95	below_threshold
Flavobacterium frigoris	strain=DSM 15719	GCA_900111075.1	229204	229204	type	True	88.5367	977	1336	95	below_threshold
Flavobacterium hiemivividum	strain=TSA-D2	GCA_004349145.1	2541734	2541734	type	True	84.0579	823	1336	95	below_threshold
Flavobacterium degerlachei	strain=DSM 15718	GCA_900106645.1	229203	229203	type	True	81.7643	741	1336	95	below_threshold
Flavobacterium muglaense	strain=F-60	GCA_014305155.1	2764716	2764716	type	True	80.4683	597	1336	95	below_threshold
Flavobacterium granuli	strain=DSM 17797	GCA_003003155.1	280093	280093	type	True	80.2566	544	1336	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	80.029	595	1336	95	below_threshold
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	79.994	536	1336	95	below_threshold
Flavobacterium frigidarium	strain=DSM 17623	GCA_000425505.1	99286	99286	type	True	79.9109	489	1336	95	below_threshold
Flavobacterium urumqiense	strain=CGMCC 1.9230	GCA_900108015.1	935224	935224	type	True	79.8827	566	1336	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	79.6965	578	1336	95	below_threshold
Flavobacterium glaciei	strain=CGMCC 1.5380	GCA_007994155.1	386300	386300	type	True	79.4861	518	1336	95	below_threshold
Flavobacterium glaciei	strain=DSM 19728	GCA_003350545.1	386300	386300	type	True	79.4498	520	1336	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	78.4101	435	1336	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.2945	354	1336	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.1215	372	1336	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:02:27,772] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6772/tc_result.tsv
[2023-03-15 21:02:27,772] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:02:27,772] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:02:27,772] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b774387-2702-41e3-9ec6-1ebbb322cf34/dqc_reference/checkm_data
[2023-03-15 21:02:27,773] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:02:27,778] [INFO] Task started: CheckM
[2023-03-15 21:02:27,778] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6772/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6772/checkm_input OceanDNA-b6772/checkm_result
[2023-03-15 21:03:32,025] [INFO] Task succeeded: CheckM
[2023-03-15 21:03:32,026] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:03:32,028] [INFO] ===== Completeness check finished =====
[2023-03-15 21:03:32,028] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:03:32,029] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6772/markers.fasta)
[2023-03-15 21:03:32,029] [INFO] Task started: Blastn
[2023-03-15 21:03:32,029] [INFO] Running command: blastn -query OceanDNA-b6772/markers.fasta -db /var/lib/cwl/stg5b774387-2702-41e3-9ec6-1ebbb322cf34/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6772/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:03:32,900] [INFO] Task succeeded: Blastn
[2023-03-15 21:03:32,900] [INFO] Selected 7 target genomes.
[2023-03-15 21:03:32,900] [INFO] Target genome list was writen to OceanDNA-b6772/target_genomes_gtdb.txt
[2023-03-15 21:03:33,060] [INFO] Task started: fastANI
[2023-03-15 21:03:33,060] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c13585d-c552-4064-b9d4-c48df5e7f82a/OceanDNA-b6772.fa --refList OceanDNA-b6772/target_genomes_gtdb.txt --output OceanDNA-b6772/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:03:39,287] [INFO] Task succeeded: fastANI
[2023-03-15 21:03:39,292] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:03:39,292] [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_900107635.1	s__Flavobacterium gillisiae	93.5036	1110	1336	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111075.1	s__Flavobacterium frigoris	88.5489	976	1336	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836475.1	s__Flavobacterium sp002836475	85.8874	883	1336	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000264055.1	s__Flavobacterium sp000264055	84.5807	843	1336	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349145.1	s__Flavobacterium hiemivividum	84.0638	822	1336	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	95.37	95.37	0.86	0.86	2	-
GCF_014305155.1	s__Flavobacterium sp014305155	80.4829	596	1336	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013294025.1	s__Flavobacterium sp013294025	79.6196	479	1336	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:03:39,292] [INFO] GTDB search result was written to OceanDNA-b6772/result_gtdb.tsv
[2023-03-15 21:03:39,292] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:03:39,294] [INFO] DFAST_QC result json was written to OceanDNA-b6772/dqc_result.json
[2023-03-15 21:03:39,294] [INFO] DFAST_QC completed!
[2023-03-15 21:03:39,294] [INFO] Total running time: 0h1m55s