[2023-03-18 01:08:39,140] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:08:39,140] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:08:39,140] [INFO] DQC Reference Directory: /var/lib/cwl/stg876c4cb1-cdac-437f-92de-ce0947622d05/dqc_reference
[2023-03-18 01:08:40,235] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:08:40,235] [INFO] Task started: Prodigal
[2023-03-18 01:08:40,235] [INFO] Running command: cat /var/lib/cwl/stg9a15c966-f106-4e52-958d-dcb7666cd924/OceanDNA-b34523.fa | prodigal -d OceanDNA-b34523/cds.fna -a OceanDNA-b34523/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:08:48,588] [INFO] Task succeeded: Prodigal
[2023-03-18 01:08:48,589] [INFO] Task started: HMMsearch
[2023-03-18 01:08:48,589] [INFO] Running command: hmmsearch --tblout OceanDNA-b34523/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg876c4cb1-cdac-437f-92de-ce0947622d05/dqc_reference/reference_markers.hmm OceanDNA-b34523/protein.faa > /dev/null
[2023-03-18 01:08:48,778] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:08:48,778] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9a15c966-f106-4e52-958d-dcb7666cd924/OceanDNA-b34523.fa]
[2023-03-18 01:08:48,802] [INFO] Query marker FASTA was written to OceanDNA-b34523/markers.fasta
[2023-03-18 01:08:48,803] [INFO] Task started: Blastn
[2023-03-18 01:08:48,803] [INFO] Running command: blastn -query OceanDNA-b34523/markers.fasta -db /var/lib/cwl/stg876c4cb1-cdac-437f-92de-ce0947622d05/dqc_reference/reference_markers.fasta -out OceanDNA-b34523/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:08:49,395] [INFO] Task succeeded: Blastn
[2023-03-18 01:08:49,397] [INFO] Selected 15 target genomes.
[2023-03-18 01:08:49,397] [INFO] Target genome list was writen to OceanDNA-b34523/target_genomes.txt
[2023-03-18 01:08:49,404] [INFO] Task started: fastANI
[2023-03-18 01:08:49,404] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a15c966-f106-4e52-958d-dcb7666cd924/OceanDNA-b34523.fa --refList OceanDNA-b34523/target_genomes.txt --output OceanDNA-b34523/fastani_result.tsv --threads 1
[2023-03-18 01:08:59,666] [INFO] Task succeeded: fastANI
[2023-03-18 01:08:59,666] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg876c4cb1-cdac-437f-92de-ce0947622d05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:08:59,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg876c4cb1-cdac-437f-92de-ce0947622d05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:08:59,672] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:08:59,672] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:08:59,672] [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
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	94.1453	252	296	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	89.3409	251	296	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	89.0721	244	296	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	84.8732	209	296	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	83.6556	215	296	95	below_threshold
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	79.6121	86	296	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:08:59,674] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34523/tc_result.tsv
[2023-03-18 01:08:59,676] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:08:59,676] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:08:59,676] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg876c4cb1-cdac-437f-92de-ce0947622d05/dqc_reference/checkm_data
[2023-03-18 01:08:59,677] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:08:59,685] [INFO] Task started: CheckM
[2023-03-18 01:08:59,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34523/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34523/checkm_input OceanDNA-b34523/checkm_result
[2023-03-18 01:09:26,404] [INFO] Task succeeded: CheckM
[2023-03-18 01:09:26,404] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.45%
Contamintation: 1.88%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-18 01:09:26,408] [INFO] ===== Completeness check finished =====
[2023-03-18 01:09:26,408] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:09:26,409] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34523/markers.fasta)
[2023-03-18 01:09:26,410] [INFO] Task started: Blastn
[2023-03-18 01:09:26,410] [INFO] Running command: blastn -query OceanDNA-b34523/markers.fasta -db /var/lib/cwl/stg876c4cb1-cdac-437f-92de-ce0947622d05/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34523/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:09:27,241] [INFO] Task succeeded: Blastn
[2023-03-18 01:09:27,242] [INFO] Selected 11 target genomes.
[2023-03-18 01:09:27,242] [INFO] Target genome list was writen to OceanDNA-b34523/target_genomes_gtdb.txt
[2023-03-18 01:09:27,259] [INFO] Task started: fastANI
[2023-03-18 01:09:27,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a15c966-f106-4e52-958d-dcb7666cd924/OceanDNA-b34523.fa --refList OceanDNA-b34523/target_genomes_gtdb.txt --output OceanDNA-b34523/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:09:34,793] [INFO] Task succeeded: fastANI
[2023-03-18 01:09:34,800] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:09:34,801] [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_000808575.1	s__Alteromonas marina	97.3453	263	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.44	97.44	0.91	0.91	2	conclusive
GCF_000172635.2	s__Alteromonas macleodii	94.1453	252	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.79	96.10	0.88	0.76	56	-
GCF_001953635.1	s__Alteromonas abrolhosensis	89.3409	251	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.27	97.25	0.92	0.89	10	-
GCF_005117025.1	s__Alteromonas portus	89.0721	244	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001885075.1	s__Alteromonas sp001885075	86.8987	183	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903772925.1	s__Alteromonas macleodii_A	85.6108	233	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003443615.1	s__Alteromonas sp003443615	84.9971	237	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000597705.1	s__Alteromonas sp000597705	84.9588	240	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.20	99.20	0.96	0.96	2	-
GCF_009811415.1	s__Alteromonas sp009811415	84.5098	199	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016405965.1	s__Alteromonas sp016405965	84.0546	197	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993325.1	s__Alteromonas gracilis	83.6423	215	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	96.94	96.21	0.87	0.84	4	-
--------------------------------------------------------------------------------
[2023-03-18 01:09:34,801] [INFO] GTDB search result was written to OceanDNA-b34523/result_gtdb.tsv
[2023-03-18 01:09:34,802] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:09:34,804] [INFO] DFAST_QC result json was written to OceanDNA-b34523/dqc_result.json
[2023-03-18 01:09:34,804] [INFO] DFAST_QC completed!
[2023-03-18 01:09:34,804] [INFO] Total running time: 0h0m56s