[2023-03-15 12:33:51,678] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:33:51,678] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:33:51,679] [INFO] DQC Reference Directory: /var/lib/cwl/stg56c52a21-0ea9-49f0-947f-8a4207eaa98a/dqc_reference
[2023-03-15 12:33:52,769] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:33:52,769] [INFO] Task started: Prodigal
[2023-03-15 12:33:52,770] [INFO] Running command: cat /var/lib/cwl/stgce31b392-89fa-45fd-b2fe-cd45f57836e6/OceanDNA-b41226.fa | prodigal -d OceanDNA-b41226/cds.fna -a OceanDNA-b41226/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:34:08,105] [INFO] Task succeeded: Prodigal
[2023-03-15 12:34:08,105] [INFO] Task started: HMMsearch
[2023-03-15 12:34:08,105] [INFO] Running command: hmmsearch --tblout OceanDNA-b41226/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56c52a21-0ea9-49f0-947f-8a4207eaa98a/dqc_reference/reference_markers.hmm OceanDNA-b41226/protein.faa > /dev/null
[2023-03-15 12:34:08,292] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:34:08,293] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgce31b392-89fa-45fd-b2fe-cd45f57836e6/OceanDNA-b41226.fa]
[2023-03-15 12:34:08,314] [INFO] Query marker FASTA was written to OceanDNA-b41226/markers.fasta
[2023-03-15 12:34:08,314] [INFO] Task started: Blastn
[2023-03-15 12:34:08,314] [INFO] Running command: blastn -query OceanDNA-b41226/markers.fasta -db /var/lib/cwl/stg56c52a21-0ea9-49f0-947f-8a4207eaa98a/dqc_reference/reference_markers.fasta -out OceanDNA-b41226/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:34:08,980] [INFO] Task succeeded: Blastn
[2023-03-15 12:34:08,982] [INFO] Selected 11 target genomes.
[2023-03-15 12:34:08,983] [INFO] Target genome list was writen to OceanDNA-b41226/target_genomes.txt
[2023-03-15 12:34:08,990] [INFO] Task started: fastANI
[2023-03-15 12:34:08,990] [INFO] Running command: fastANI --query /var/lib/cwl/stgce31b392-89fa-45fd-b2fe-cd45f57836e6/OceanDNA-b41226.fa --refList OceanDNA-b41226/target_genomes.txt --output OceanDNA-b41226/fastani_result.tsv --threads 1
[2023-03-15 12:34:19,034] [INFO] Task succeeded: fastANI
[2023-03-15 12:34:19,034] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56c52a21-0ea9-49f0-947f-8a4207eaa98a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:34:19,034] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56c52a21-0ea9-49f0-947f-8a4207eaa98a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:34:19,041] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:34:19,041] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 12:34:19,042] [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
Pseudomonas peli	strain=DSM 17833	GCA_012986145.1	592361	592361	type	True	88.0544	681	821	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_900099645.1	592361	592361	type	True	87.9482	678	821	95	below_threshold
Pseudomonas guineae	strain=LMG 24016	GCA_900113745.1	425504	425504	type	True	83.6432	609	821	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	82.3035	564	821	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	82.1651	539	821	95	below_threshold
Pseudomonas cuatrocienegasensis	strain=CIP 109853	GCA_900110925.1	543360	543360	type	True	81.9513	535	821	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	81.841	604	821	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	81.5185	530	821	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	81.3829	510	821	95	below_threshold
Pseudomonas taeanensis	strain=MS-3	GCA_000498575.2	574962	574962	type	True	81.1338	517	821	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	80.9866	482	821	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:34:19,043] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41226/tc_result.tsv
[2023-03-15 12:34:19,043] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:34:19,043] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:34:19,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56c52a21-0ea9-49f0-947f-8a4207eaa98a/dqc_reference/checkm_data
[2023-03-15 12:34:19,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:34:19,049] [INFO] Task started: CheckM
[2023-03-15 12:34:19,049] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41226/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41226/checkm_input OceanDNA-b41226/checkm_result
[2023-03-15 12:34:59,843] [INFO] Task succeeded: CheckM
[2023-03-15 12:34:59,843] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:34:59,866] [INFO] ===== Completeness check finished =====
[2023-03-15 12:34:59,867] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:34:59,867] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41226/markers.fasta)
[2023-03-15 12:34:59,868] [INFO] Task started: Blastn
[2023-03-15 12:34:59,868] [INFO] Running command: blastn -query OceanDNA-b41226/markers.fasta -db /var/lib/cwl/stg56c52a21-0ea9-49f0-947f-8a4207eaa98a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41226/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:35:00,886] [INFO] Task succeeded: Blastn
[2023-03-15 12:35:00,892] [INFO] Selected 11 target genomes.
[2023-03-15 12:35:00,892] [INFO] Target genome list was writen to OceanDNA-b41226/target_genomes_gtdb.txt
[2023-03-15 12:35:01,034] [INFO] Task started: fastANI
[2023-03-15 12:35:01,034] [INFO] Running command: fastANI --query /var/lib/cwl/stgce31b392-89fa-45fd-b2fe-cd45f57836e6/OceanDNA-b41226.fa --refList OceanDNA-b41226/target_genomes_gtdb.txt --output OceanDNA-b41226/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:35:10,792] [INFO] Task succeeded: fastANI
[2023-03-15 12:35:10,799] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:35:10,799] [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_002840155.1	s__Pseudomonas_E sp002840155	89.5894	720	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105355.1	s__Pseudomonas_E anguilliseptica	89.3262	715	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.12	96.12	0.88	0.88	2	-
GCA_018827205.1	s__Pseudomonas_E sp018827205	88.1503	657	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.54	99.51	0.89	0.88	4	-
GCF_900099645.1	s__Pseudomonas_E peli	87.9643	677	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.85	96.04	0.90	0.85	7	-
GCF_003060885.1	s__Pseudomonas_E sp003060885	86.1905	650	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004920405.1	s__Pseudomonas_E leptonychotis	85.1845	674	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018816095.1	s__Pseudomonas_E sp018816095	84.5628	567	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.20	96.15	0.83	0.82	4	-
GCF_900113745.1	s__Pseudomonas_E guineae	83.6545	608	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001465025.1	s__Pseudomonas_E sp001465025	83.1601	539	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.96	95.96	0.61	0.61	2	-
GCF_009763245.1	s__Pseudomonas_E sp009763245	82.9531	578	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002354655.1	s__Pseudomonas_E sp002354655	82.9362	600	821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.84	99.84	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-03-15 12:35:10,802] [INFO] GTDB search result was written to OceanDNA-b41226/result_gtdb.tsv
[2023-03-15 12:35:10,806] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:35:10,809] [INFO] DFAST_QC result json was written to OceanDNA-b41226/dqc_result.json
[2023-03-15 12:35:10,809] [INFO] DFAST_QC completed!
[2023-03-15 12:35:10,809] [INFO] Total running time: 0h1m19s