[2023-03-18 21:15:29,377] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:15:29,377] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:15:29,378] [INFO] DQC Reference Directory: /var/lib/cwl/stgdee19e8e-1d70-4d33-90ba-36ce861ce701/dqc_reference
[2023-03-18 21:15:31,045] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:15:31,045] [INFO] Task started: Prodigal
[2023-03-18 21:15:31,046] [INFO] Running command: cat /var/lib/cwl/stg5609418d-6646-40f3-89df-1b1604d40563/OceanDNA-b36441.fa | prodigal -d OceanDNA-b36441/cds.fna -a OceanDNA-b36441/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:15:56,301] [INFO] Task succeeded: Prodigal
[2023-03-18 21:15:56,301] [INFO] Task started: HMMsearch
[2023-03-18 21:15:56,301] [INFO] Running command: hmmsearch --tblout OceanDNA-b36441/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdee19e8e-1d70-4d33-90ba-36ce861ce701/dqc_reference/reference_markers.hmm OceanDNA-b36441/protein.faa > /dev/null
[2023-03-18 21:15:56,526] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:15:56,526] [INFO] Found 6/6 markers.
[2023-03-18 21:15:56,554] [INFO] Query marker FASTA was written to OceanDNA-b36441/markers.fasta
[2023-03-18 21:15:56,554] [INFO] Task started: Blastn
[2023-03-18 21:15:56,554] [INFO] Running command: blastn -query OceanDNA-b36441/markers.fasta -db /var/lib/cwl/stgdee19e8e-1d70-4d33-90ba-36ce861ce701/dqc_reference/reference_markers.fasta -out OceanDNA-b36441/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:15:57,387] [INFO] Task succeeded: Blastn
[2023-03-18 21:15:57,389] [INFO] Selected 10 target genomes.
[2023-03-18 21:15:57,389] [INFO] Target genome list was writen to OceanDNA-b36441/target_genomes.txt
[2023-03-18 21:15:57,396] [INFO] Task started: fastANI
[2023-03-18 21:15:57,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg5609418d-6646-40f3-89df-1b1604d40563/OceanDNA-b36441.fa --refList OceanDNA-b36441/target_genomes.txt --output OceanDNA-b36441/fastani_result.tsv --threads 1
[2023-03-18 21:16:07,189] [INFO] Task succeeded: fastANI
[2023-03-18 21:16:07,189] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdee19e8e-1d70-4d33-90ba-36ce861ce701/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:16:07,190] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdee19e8e-1d70-4d33-90ba-36ce861ce701/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:16:07,197] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 21:16:07,197] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 21:16:07,197] [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
Alcanivorax mobilis	strain=MT13131	GCA_002864685.1	2019569	2019569	type	True	98.6986	1199	1298	95	conclusive
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	82.7216	778	1298	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	82.4869	817	1298	95	below_threshold
Alcanivorax venustensis	strain=ISO4	GCA_015356855.1	172371	172371	type	True	82.4576	794	1298	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	82.4529	830	1298	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	79.777	658	1298	95	below_threshold
Alcanivorax xenomutans	strain=JC109	GCA_900217905.1	1094342	1094342	type	True	79.6557	627	1298	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	77.4597	277	1298	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.2336	237	1298	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	76.1568	105	1298	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:16:07,199] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36441/tc_result.tsv
[2023-03-18 21:16:07,199] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:16:07,199] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:16:07,199] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdee19e8e-1d70-4d33-90ba-36ce861ce701/dqc_reference/checkm_data
[2023-03-18 21:16:07,200] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:16:07,207] [INFO] Task started: CheckM
[2023-03-18 21:16:07,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36441/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36441/checkm_input OceanDNA-b36441/checkm_result
[2023-03-18 21:17:09,587] [INFO] Task succeeded: CheckM
[2023-03-18 21:17:09,587] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:17:09,607] [INFO] ===== Completeness check finished =====
[2023-03-18 21:17:09,608] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:17:09,608] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36441/markers.fasta)
[2023-03-18 21:17:09,609] [INFO] Task started: Blastn
[2023-03-18 21:17:09,609] [INFO] Running command: blastn -query OceanDNA-b36441/markers.fasta -db /var/lib/cwl/stgdee19e8e-1d70-4d33-90ba-36ce861ce701/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36441/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:17:11,150] [INFO] Task succeeded: Blastn
[2023-03-18 21:17:11,154] [INFO] Selected 8 target genomes.
[2023-03-18 21:17:11,154] [INFO] Target genome list was writen to OceanDNA-b36441/target_genomes_gtdb.txt
[2023-03-18 21:17:11,164] [INFO] Task started: fastANI
[2023-03-18 21:17:11,164] [INFO] Running command: fastANI --query /var/lib/cwl/stg5609418d-6646-40f3-89df-1b1604d40563/OceanDNA-b36441.fa --refList OceanDNA-b36441/target_genomes_gtdb.txt --output OceanDNA-b36441/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:17:18,842] [INFO] Task succeeded: fastANI
[2023-03-18 21:17:18,847] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:17:18,847] [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_002864685.1	s__Alcanivorax mobilis	98.6986	1199	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.57	98.57	0.96	0.96	2	conclusive
GCF_016906305.1	s__Alcanivorax marinus_B	82.6114	842	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015356855.1	s__Alcanivorax venustensis	82.4561	794	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.73	95.38	0.91	0.87	46	-
GCF_015265435.1	s__Alcanivorax profundimaris	82.4544	820	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.49	97.23	0.85	0.77	11	-
GCF_005938655.1	s__Alcanivorax gelatiniphagus	82.4202	833	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.53	98.53	0.93	0.93	3	-
GCA_017794945.1	s__Alcanivorax sp009711585	82.2281	711	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	96.99	96.99	0.93	0.93	2	-
GCA_002389055.1	s__Alcanivorax sp002389055	81.5905	666	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	96.98	96.27	0.78	0.74	3	-
GCF_016785095.1	s__Alcanivorax marinus_A	81.4778	798	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:17:18,849] [INFO] GTDB search result was written to OceanDNA-b36441/result_gtdb.tsv
[2023-03-18 21:17:18,850] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:17:18,852] [INFO] DFAST_QC result json was written to OceanDNA-b36441/dqc_result.json
[2023-03-18 21:17:18,852] [INFO] DFAST_QC completed!
[2023-03-18 21:17:18,852] [INFO] Total running time: 0h1m49s