[2023-03-16 04:35:06,184] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:35:06,184] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:35:06,184] [INFO] DQC Reference Directory: /var/lib/cwl/stg44cb2641-7930-4ff6-837b-78875bc3af78/dqc_reference
[2023-03-16 04:35:07,267] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:35:07,267] [INFO] Task started: Prodigal
[2023-03-16 04:35:07,267] [INFO] Running command: cat /var/lib/cwl/stg9065566f-b675-491b-a1c3-c0eb9ac1ad14/OceanDNA-b41211.fa | prodigal -d OceanDNA-b41211/cds.fna -a OceanDNA-b41211/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:35:27,976] [INFO] Task succeeded: Prodigal
[2023-03-16 04:35:27,976] [INFO] Task started: HMMsearch
[2023-03-16 04:35:27,976] [INFO] Running command: hmmsearch --tblout OceanDNA-b41211/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44cb2641-7930-4ff6-837b-78875bc3af78/dqc_reference/reference_markers.hmm OceanDNA-b41211/protein.faa > /dev/null
[2023-03-16 04:35:28,179] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:35:28,180] [INFO] Found 6/6 markers.
[2023-03-16 04:35:28,202] [INFO] Query marker FASTA was written to OceanDNA-b41211/markers.fasta
[2023-03-16 04:35:28,202] [INFO] Task started: Blastn
[2023-03-16 04:35:28,203] [INFO] Running command: blastn -query OceanDNA-b41211/markers.fasta -db /var/lib/cwl/stg44cb2641-7930-4ff6-837b-78875bc3af78/dqc_reference/reference_markers.fasta -out OceanDNA-b41211/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:35:28,981] [INFO] Task succeeded: Blastn
[2023-03-16 04:35:28,982] [INFO] Selected 25 target genomes.
[2023-03-16 04:35:28,982] [INFO] Target genome list was writen to OceanDNA-b41211/target_genomes.txt
[2023-03-16 04:35:28,994] [INFO] Task started: fastANI
[2023-03-16 04:35:28,994] [INFO] Running command: fastANI --query /var/lib/cwl/stg9065566f-b675-491b-a1c3-c0eb9ac1ad14/OceanDNA-b41211.fa --refList OceanDNA-b41211/target_genomes.txt --output OceanDNA-b41211/fastani_result.tsv --threads 1
[2023-03-16 04:35:46,099] [INFO] Task succeeded: fastANI
[2023-03-16 04:35:46,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44cb2641-7930-4ff6-837b-78875bc3af78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:35:46,100] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44cb2641-7930-4ff6-837b-78875bc3af78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:35:46,113] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:35:46,113] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:35:46,113] [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
Halopseudomonas salina	strain=CGMCC 1.12482	GCA_014637955.1	1323744	1323744	type	True	79.135	423	1111	95	below_threshold
Pseudomonas yangmingensis	strain=DSM 24213	GCA_900114825.1	1720063	1720063	type	True	79.0975	413	1111	95	below_threshold
Halopseudomonas salina	strain=XCD-X85	GCA_008641105.1	1323744	1323744	type	True	79.0932	432	1111	95	below_threshold
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	78.9242	366	1111	95	below_threshold
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	78.9142	411	1111	95	below_threshold
Halopseudomonas bauzanensis	strain=CGMCC 1.9095	GCA_900114735.1	653930	653930	type	True	78.8787	360	1111	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	78.8753	426	1111	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	78.8672	401	1111	95	below_threshold
Halopseudomonas litoralis	strain=2SM5	GCA_900105005.1	797277	797277	type	True	78.8565	354	1111	95	below_threshold
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	78.8539	438	1111	95	below_threshold
Halopseudomonas oceani	strain=DSM 100277	GCA_002903165.1	1708783	1708783	type	True	78.7882	384	1111	95	below_threshold
Halopseudomonas oceani	strain=CGMCC 1.15195	GCA_014641295.1	1708783	1708783	type	True	78.7772	385	1111	95	below_threshold
Pseudomonas profundi	strain=M5	GCA_008638305.1	1981513	1981513	type	True	78.4618	322	1111	95	below_threshold
Pseudomonas saliphila	strain=16W4-4-3	GCA_008638345.1	2586906	2586906	type	True	78.1587	341	1111	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	78.0931	264	1111	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	78.0109	226	1111	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	77.9554	264	1111	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	77.761	246	1111	95	below_threshold
Azotobacter chroococcum	strain=ATCC 9043	GCA_004327905.1	353	353	type	True	77.7514	203	1111	95	below_threshold
Azotobacter chroococcum	strain=DSM 2286	GCA_004339665.1	353	353	type	True	77.7352	203	1111	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	77.6765	206	1111	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_012987025.1	287	287	type	True	77.602	241	1111	95	below_threshold
Pseudomonas cuatrocienegasensis	strain=CIP 109853	GCA_900110925.1	543360	543360	type	True	77.573	261	1111	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_900167195.1	287	287	type	True	77.5526	243	1111	95	below_threshold
Pseudomonas cavernicola	strain=K1S02-6	GCA_003596405.1	2320866	2320866	type	True	77.5383	212	1111	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:35:46,113] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41211/tc_result.tsv
[2023-03-16 04:35:46,113] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:35:46,113] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:35:46,114] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44cb2641-7930-4ff6-837b-78875bc3af78/dqc_reference/checkm_data
[2023-03-16 04:35:46,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:35:46,122] [INFO] Task started: CheckM
[2023-03-16 04:35:46,122] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41211/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41211/checkm_input OceanDNA-b41211/checkm_result
[2023-03-16 04:36:38,810] [INFO] Task succeeded: CheckM
[2023-03-16 04:36:38,811] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:36:38,833] [INFO] ===== Completeness check finished =====
[2023-03-16 04:36:38,834] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:36:38,834] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41211/markers.fasta)
[2023-03-16 04:36:38,835] [INFO] Task started: Blastn
[2023-03-16 04:36:38,835] [INFO] Running command: blastn -query OceanDNA-b41211/markers.fasta -db /var/lib/cwl/stg44cb2641-7930-4ff6-837b-78875bc3af78/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41211/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:36:40,233] [INFO] Task succeeded: Blastn
[2023-03-16 04:36:40,234] [INFO] Selected 17 target genomes.
[2023-03-16 04:36:40,234] [INFO] Target genome list was writen to OceanDNA-b41211/target_genomes_gtdb.txt
[2023-03-16 04:36:40,248] [INFO] Task started: fastANI
[2023-03-16 04:36:40,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg9065566f-b675-491b-a1c3-c0eb9ac1ad14/OceanDNA-b41211.fa --refList OceanDNA-b41211/target_genomes_gtdb.txt --output OceanDNA-b41211/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:36:52,854] [INFO] Task succeeded: fastANI
[2023-03-16 04:36:52,864] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:36:52,864] [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_002840055.1	s__Pseudomonas_D sp002840055	98.0923	719	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008365385.1	s__Pseudomonas_D laoshanensis	80.0005	500	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.00	95.95	0.96	0.95	3	-
GCF_009497895.1	s__Pseudomonas_D pelagia_A	79.9342	514	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000410875.1	s__Pseudomonas_D pelagia	79.7494	517	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000939975.1	s__Pseudomonas_D saudimassiliensis	79.3275	369	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008641105.1	s__Pseudomonas_D salina	79.1214	426	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002979975.1	s__Pseudomonas_D sp002979975	79.0395	398	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116555.1	s__Pseudomonas_D excrementavium	78.9711	304	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105655.1	s__Pseudomonas_D salegens	78.9272	427	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763285.1	s__Pseudomonas_D sp016763285	78.8689	368	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114735.1	s__Pseudomonas_D bauzanensis	78.8664	361	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	99.15	98.30	0.96	0.91	3	-
GCF_900105005.1	s__Pseudomonas_D litoralis	78.8565	354	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115905.1	s__Pseudomonas_D formosensis	78.7551	360	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	98.74	98.74	0.94	0.94	2	-
GCF_003797905.1	s__Pseudomonas_D sp002683975	78.4087	335	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	98.94	98.05	0.94	0.90	5	-
GCF_004339665.1	s__Azotobacter chroococcum	77.7544	204	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	97.27	96.18	0.89	0.83	10	-
GCF_009363155.1	s__Azotobacter salinestris	77.6115	218	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001457615.1	s__Pseudomonas aeruginosa	77.5749	242	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.12	97.38	0.94	0.84	5623	-
--------------------------------------------------------------------------------
[2023-03-16 04:36:52,864] [INFO] GTDB search result was written to OceanDNA-b41211/result_gtdb.tsv
[2023-03-16 04:36:52,864] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:36:52,867] [INFO] DFAST_QC result json was written to OceanDNA-b41211/dqc_result.json
[2023-03-16 04:36:52,867] [INFO] DFAST_QC completed!
[2023-03-16 04:36:52,867] [INFO] Total running time: 0h1m47s