[2023-03-18 08:36:16,008] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:36:16,008] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:36:16,008] [INFO] DQC Reference Directory: /var/lib/cwl/stg82e53903-49fb-44c3-9a68-834c998d070a/dqc_reference
[2023-03-18 08:36:17,827] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:36:17,827] [INFO] Task started: Prodigal
[2023-03-18 08:36:17,827] [INFO] Running command: cat /var/lib/cwl/stg65077c4a-52d1-4de8-b9a4-77058f74cc6f/OceanDNA-b34611.fa | prodigal -d OceanDNA-b34611/cds.fna -a OceanDNA-b34611/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:36:31,279] [INFO] Task succeeded: Prodigal
[2023-03-18 08:36:31,280] [INFO] Task started: HMMsearch
[2023-03-18 08:36:31,280] [INFO] Running command: hmmsearch --tblout OceanDNA-b34611/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82e53903-49fb-44c3-9a68-834c998d070a/dqc_reference/reference_markers.hmm OceanDNA-b34611/protein.faa > /dev/null
[2023-03-18 08:36:31,524] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:36:31,525] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg65077c4a-52d1-4de8-b9a4-77058f74cc6f/OceanDNA-b34611.fa]
[2023-03-18 08:36:31,550] [INFO] Query marker FASTA was written to OceanDNA-b34611/markers.fasta
[2023-03-18 08:36:31,550] [INFO] Task started: Blastn
[2023-03-18 08:36:31,550] [INFO] Running command: blastn -query OceanDNA-b34611/markers.fasta -db /var/lib/cwl/stg82e53903-49fb-44c3-9a68-834c998d070a/dqc_reference/reference_markers.fasta -out OceanDNA-b34611/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:36:32,113] [INFO] Task succeeded: Blastn
[2023-03-18 08:36:32,114] [INFO] Selected 21 target genomes.
[2023-03-18 08:36:32,114] [INFO] Target genome list was writen to OceanDNA-b34611/target_genomes.txt
[2023-03-18 08:36:32,162] [INFO] Task started: fastANI
[2023-03-18 08:36:32,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg65077c4a-52d1-4de8-b9a4-77058f74cc6f/OceanDNA-b34611.fa --refList OceanDNA-b34611/target_genomes.txt --output OceanDNA-b34611/fastani_result.tsv --threads 1
[2023-03-18 08:36:47,075] [INFO] Task succeeded: fastANI
[2023-03-18 08:36:47,075] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82e53903-49fb-44c3-9a68-834c998d070a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:36:47,075] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82e53903-49fb-44c3-9a68-834c998d070a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:36:47,085] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:36:47,085] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:36:47,085] [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 confluentis	strain=KCTC 42603	GCA_001757105.1	1656094	1656094	type	True	81.6679	315	648	95	below_threshold
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	77.5139	117	648	95	below_threshold
Alteromonas oceani	strain=S35	GCA_003731635.1	2071609	2071609	type	True	77.4982	102	648	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	77.4525	87	648	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	77.4322	91	648	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	77.429	85	648	95	below_threshold
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	77.32	109	648	95	below_threshold
Alteromonas aestuariivivens	strain=KCTC 52655	GCA_003367475.1	1938339	1938339	type	True	77.2826	94	648	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	77.2825	136	648	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	77.2456	83	648	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	77.1657	78	648	95	below_threshold
Salinimonas profundi	strain=HHU 13199	GCA_014750655.1	2729140	2729140	type	True	77.1022	96	648	95	below_threshold
Alteromonas profundi	strain=345S023	GCA_010500865.1	2696062	2696062	type	True	77.0853	72	648	95	below_threshold
Alteromonas naphthalenivorans	strain=SN2	GCA_000213655.1	715451	715451	type	True	76.9389	79	648	95	below_threshold
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	76.8839	80	648	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:36:47,085] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34611/tc_result.tsv
[2023-03-18 08:36:47,085] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:36:47,085] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:36:47,085] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82e53903-49fb-44c3-9a68-834c998d070a/dqc_reference/checkm_data
[2023-03-18 08:36:47,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:36:47,092] [INFO] Task started: CheckM
[2023-03-18 08:36:47,092] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34611/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34611/checkm_input OceanDNA-b34611/checkm_result
[2023-03-18 08:37:24,949] [INFO] Task succeeded: CheckM
[2023-03-18 08:37:24,950] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:37:24,954] [INFO] ===== Completeness check finished =====
[2023-03-18 08:37:24,954] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:37:24,954] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34611/markers.fasta)
[2023-03-18 08:37:24,955] [INFO] Task started: Blastn
[2023-03-18 08:37:24,955] [INFO] Running command: blastn -query OceanDNA-b34611/markers.fasta -db /var/lib/cwl/stg82e53903-49fb-44c3-9a68-834c998d070a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34611/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:37:25,781] [INFO] Task succeeded: Blastn
[2023-03-18 08:37:25,784] [INFO] Selected 19 target genomes.
[2023-03-18 08:37:25,784] [INFO] Target genome list was writen to OceanDNA-b34611/target_genomes_gtdb.txt
[2023-03-18 08:37:25,819] [INFO] Task started: fastANI
[2023-03-18 08:37:25,819] [INFO] Running command: fastANI --query /var/lib/cwl/stg65077c4a-52d1-4de8-b9a4-77058f74cc6f/OceanDNA-b34611.fa --refList OceanDNA-b34611/target_genomes_gtdb.txt --output OceanDNA-b34611/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:37:38,881] [INFO] Task succeeded: fastANI
[2023-03-18 08:37:38,892] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:37:38,892] [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_003584565.2	s__Alteromonas sp002729795	97.2619	613	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.21	97.21	0.92	0.92	2	conclusive
GCF_001757105.1	s__Alteromonas confluentis	81.6679	315	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860965.1	s__Alteromonas sp018860965	78.773	157	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000808575.1	s__Alteromonas marina	77.5798	83	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.44	97.44	0.91	0.91	2	-
GCF_900129565.1	s__Alteromonas aggregata	77.5157	109	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.34	96.39	0.91	0.85	11	-
GCA_019249295.1	s__Alteromonas antoniana	77.5139	117	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003731635.1	s__Alteromonas oceani	77.4982	102	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953635.1	s__Alteromonas abrolhosensis	77.4525	87	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.27	97.25	0.92	0.89	10	-
GCF_002993325.1	s__Alteromonas gracilis	77.4322	91	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	96.94	96.21	0.87	0.84	4	-
GCF_000172635.2	s__Alteromonas macleodii	77.429	85	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.79	96.10	0.88	0.76	56	-
GCF_016405965.1	s__Alteromonas sp016405965	77.3721	86	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993365.1	s__Alteromonas alba	77.32	109	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222225.1	s__Alteromonas lutimaris	77.3022	135	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691625.1	s__Alteromonas sp002691625	77.2408	80	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.62	99.31	0.91	0.90	3	-
GCF_005117025.1	s__Alteromonas portus	77.1657	78	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014750655.1	s__Alteromonas profundi_A	77.1283	95	648	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	77.1082	81	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222405.1	s__Alteromonas sp018222405	77.0209	102	648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:37:38,894] [INFO] GTDB search result was written to OceanDNA-b34611/result_gtdb.tsv
[2023-03-18 08:37:38,895] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:37:38,899] [INFO] DFAST_QC result json was written to OceanDNA-b34611/dqc_result.json
[2023-03-18 08:37:38,899] [INFO] DFAST_QC completed!
[2023-03-18 08:37:38,899] [INFO] Total running time: 0h1m23s