[2023-03-15 14:29:06,036] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:29:06,036] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:29:06,036] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b6468d6-28fc-414a-9afe-4a7c7b7a5409/dqc_reference
[2023-03-15 14:29:07,123] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:29:07,123] [INFO] Task started: Prodigal
[2023-03-15 14:29:07,123] [INFO] Running command: cat /var/lib/cwl/stg9c17e055-0349-4dfb-9a93-65d51d749e1a/OceanDNA-b20990.fa | prodigal -d OceanDNA-b20990/cds.fna -a OceanDNA-b20990/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:29:30,761] [INFO] Task succeeded: Prodigal
[2023-03-15 14:29:30,761] [INFO] Task started: HMMsearch
[2023-03-15 14:29:30,761] [INFO] Running command: hmmsearch --tblout OceanDNA-b20990/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b6468d6-28fc-414a-9afe-4a7c7b7a5409/dqc_reference/reference_markers.hmm OceanDNA-b20990/protein.faa > /dev/null
[2023-03-15 14:29:30,953] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:29:30,954] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9c17e055-0349-4dfb-9a93-65d51d749e1a/OceanDNA-b20990.fa]
[2023-03-15 14:29:30,980] [INFO] Query marker FASTA was written to OceanDNA-b20990/markers.fasta
[2023-03-15 14:29:30,982] [INFO] Task started: Blastn
[2023-03-15 14:29:30,982] [INFO] Running command: blastn -query OceanDNA-b20990/markers.fasta -db /var/lib/cwl/stg1b6468d6-28fc-414a-9afe-4a7c7b7a5409/dqc_reference/reference_markers.fasta -out OceanDNA-b20990/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:29:31,594] [INFO] Task succeeded: Blastn
[2023-03-15 14:29:31,595] [INFO] Selected 17 target genomes.
[2023-03-15 14:29:31,595] [INFO] Target genome list was writen to OceanDNA-b20990/target_genomes.txt
[2023-03-15 14:29:31,603] [INFO] Task started: fastANI
[2023-03-15 14:29:31,603] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c17e055-0349-4dfb-9a93-65d51d749e1a/OceanDNA-b20990.fa --refList OceanDNA-b20990/target_genomes.txt --output OceanDNA-b20990/fastani_result.tsv --threads 1
[2023-03-15 14:29:47,755] [INFO] Task succeeded: fastANI
[2023-03-15 14:29:47,755] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b6468d6-28fc-414a-9afe-4a7c7b7a5409/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:29:47,756] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b6468d6-28fc-414a-9afe-4a7c7b7a5409/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:29:47,762] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:29:47,762] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 14:29:47,762] [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
Corallococcus carmarthensis	strain=CA043D	GCA_003611695.1	2316728	2316728	type	True	75.0497	76	1232	95	below_threshold
Myxococcus stipitatus	strain=DSM 14675	GCA_000331735.1	83455	83455	neotype	True	74.9097	77	1232	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	74.9077	77	1232	95	below_threshold
Myxococcus fulvus	strain=NBRC 100333	GCA_007991095.1	33	33	type	True	74.8673	79	1232	95	below_threshold
Jiangella endophytica	strain=KE2-3	GCA_003427025.1	1623398	1623398	type	True	74.8046	53	1232	95	below_threshold
Jiangella anatolica	strain=GTF31	GCA_003236295.1	2670374	2670374	type	True	74.7232	58	1232	95	below_threshold
Jiangella alkaliphila	strain=DSM 45079	GCA_900105925.1	419479	419479	type	True	74.6393	52	1232	95	below_threshold
Jiangella alkaliphila	strain=KCTC 19222	GCA_001005145.1	419479	419479	type	True	74.6393	52	1232	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 14:29:47,762] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20990/tc_result.tsv
[2023-03-15 14:29:47,762] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:29:47,762] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:29:47,762] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b6468d6-28fc-414a-9afe-4a7c7b7a5409/dqc_reference/checkm_data
[2023-03-15 14:29:47,763] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:29:47,768] [INFO] Task started: CheckM
[2023-03-15 14:29:47,769] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20990/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20990/checkm_input OceanDNA-b20990/checkm_result
[2023-03-15 14:30:47,522] [INFO] Task succeeded: CheckM
[2023-03-15 14:30:47,523] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:30:47,532] [INFO] ===== Completeness check finished =====
[2023-03-15 14:30:47,532] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:30:47,532] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20990/markers.fasta)
[2023-03-15 14:30:47,533] [INFO] Task started: Blastn
[2023-03-15 14:30:47,533] [INFO] Running command: blastn -query OceanDNA-b20990/markers.fasta -db /var/lib/cwl/stg1b6468d6-28fc-414a-9afe-4a7c7b7a5409/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20990/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:30:48,457] [INFO] Task succeeded: Blastn
[2023-03-15 14:30:48,459] [INFO] Selected 16 target genomes.
[2023-03-15 14:30:48,459] [INFO] Target genome list was writen to OceanDNA-b20990/target_genomes_gtdb.txt
[2023-03-15 14:30:48,474] [INFO] Task started: fastANI
[2023-03-15 14:30:48,474] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c17e055-0349-4dfb-9a93-65d51d749e1a/OceanDNA-b20990.fa --refList OceanDNA-b20990/target_genomes_gtdb.txt --output OceanDNA-b20990/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:31:04,192] [INFO] Task succeeded: fastANI
[2023-03-15 14:31:04,199] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:31:04,200] [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_006226565.1	s__PHBI01 sp006226565	76.0046	136	1232	d__Bacteria;p__Myxococcota;c__UBA9042;o__PHBI01;f__PHBI01;g__PHBI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841945.1	s__PHBI01 sp002841945	75.9408	146	1232	d__Bacteria;p__Myxococcota;c__UBA9042;o__PHBI01;f__PHBI01;g__PHBI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792665.1	s__WYBB01 sp016792665	75.5388	93	1232	d__Bacteria;p__Myxococcota;c__UBA9042;o__PHBI01;f__PHBI01;g__WYBB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266075.1	s__SZAS-1 sp018266075	75.4356	73	1232	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__SZAS-1;g__SZAS-1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780435.1	s__SXOO01 sp018780435	75.3577	83	1232	d__Bacteria;p__Myxococcota;c__UBA9042;o__GCA-2863065;f__GCA-2863065;g__SXOO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526585.1	s__WYBB01 sp011526585	75.3419	98	1232	d__Bacteria;p__Myxococcota;c__UBA9042;o__PHBI01;f__PHBI01;g__WYBB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696455.1	s__UBA2376 sp900696455	75.1092	116	1232	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	98.40	97.29	0.91	0.90	3	-
GCA_903869075.1	s__CAIYBN01 sp903869075	75.0562	55	1232	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__CAIYBN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903911905.1	s__FEN-1143 sp903911905	74.889	50	1232	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__FEN-1143	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903906315.1	s__CAIVJW01 sp903906315	74.7806	86	1232	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAIVJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106035.1	s__Jiangella alba	74.6981	68	1232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	97.52	95.05	0.93	0.86	3	-
GCF_014636775.1	s__Kocuria dechangensis	74.6644	50	1232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 14:31:04,200] [INFO] GTDB search result was written to OceanDNA-b20990/result_gtdb.tsv
[2023-03-15 14:31:04,200] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:31:04,201] [INFO] DFAST_QC result json was written to OceanDNA-b20990/dqc_result.json
[2023-03-15 14:31:04,201] [INFO] DFAST_QC completed!
[2023-03-15 14:31:04,201] [INFO] Total running time: 0h1m58s