[2023-03-18 08:42:34,428] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:42:34,428] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:42:34,428] [INFO] DQC Reference Directory: /var/lib/cwl/stg1eb708ba-3d79-4a06-a57b-9faef2397289/dqc_reference
[2023-03-18 08:42:35,552] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:42:35,552] [INFO] Task started: Prodigal
[2023-03-18 08:42:35,553] [INFO] Running command: cat /var/lib/cwl/stg426acf0b-1e01-4a5a-a939-f2c4cc9d723c/OceanDNA-b26696.fa | prodigal -d OceanDNA-b26696/cds.fna -a OceanDNA-b26696/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:42:55,788] [INFO] Task succeeded: Prodigal
[2023-03-18 08:42:55,788] [INFO] Task started: HMMsearch
[2023-03-18 08:42:55,788] [INFO] Running command: hmmsearch --tblout OceanDNA-b26696/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1eb708ba-3d79-4a06-a57b-9faef2397289/dqc_reference/reference_markers.hmm OceanDNA-b26696/protein.faa > /dev/null
[2023-03-18 08:42:55,987] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:42:55,988] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg426acf0b-1e01-4a5a-a939-f2c4cc9d723c/OceanDNA-b26696.fa]
[2023-03-18 08:42:56,008] [INFO] Query marker FASTA was written to OceanDNA-b26696/markers.fasta
[2023-03-18 08:42:56,008] [INFO] Task started: Blastn
[2023-03-18 08:42:56,008] [INFO] Running command: blastn -query OceanDNA-b26696/markers.fasta -db /var/lib/cwl/stg1eb708ba-3d79-4a06-a57b-9faef2397289/dqc_reference/reference_markers.fasta -out OceanDNA-b26696/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:42:56,620] [INFO] Task succeeded: Blastn
[2023-03-18 08:42:56,621] [INFO] Selected 12 target genomes.
[2023-03-18 08:42:56,621] [INFO] Target genome list was writen to OceanDNA-b26696/target_genomes.txt
[2023-03-18 08:42:56,628] [INFO] Task started: fastANI
[2023-03-18 08:42:56,628] [INFO] Running command: fastANI --query /var/lib/cwl/stg426acf0b-1e01-4a5a-a939-f2c4cc9d723c/OceanDNA-b26696.fa --refList OceanDNA-b26696/target_genomes.txt --output OceanDNA-b26696/fastani_result.tsv --threads 1
[2023-03-18 08:43:05,964] [INFO] Task succeeded: fastANI
[2023-03-18 08:43:05,965] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1eb708ba-3d79-4a06-a57b-9faef2397289/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:43:05,965] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1eb708ba-3d79-4a06-a57b-9faef2397289/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:43:05,973] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:43:05,973] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:43:05,973] [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
Devosia marina	strain=L53-10-65	GCA_009758415.1	2683198	2683198	type	True	87.8568	841	1059	95	below_threshold
Devosia subaequoris	strain=DSM 23447	GCA_014197055.1	395930	395930	type	True	86.3853	827	1059	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	86.3493	830	1059	95	below_threshold
Devosia indica	strain=IO390501	GCA_003056405.1	2079253	2079253	type	True	85.6152	794	1059	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	82.98	723	1059	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	81.2486	613	1059	95	below_threshold
Devosia lucknowensis	strain=L15	GCA_900177655.1	1096929	1096929	type	True	80.3975	609	1059	95	below_threshold
Devosia faecipullorum	strain=CC-YST696	GCA_015158295.1	2755039	2755039	type	True	80.2423	540	1059	95	below_threshold
Devosia chinhatensis	strain=IPL18	GCA_000969445.1	429727	429727	type	True	80.1292	544	1059	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	79.6932	505	1059	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	79.4208	545	1059	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	79.209	489	1059	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:43:05,974] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26696/tc_result.tsv
[2023-03-18 08:43:05,975] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:43:05,975] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:43:05,975] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1eb708ba-3d79-4a06-a57b-9faef2397289/dqc_reference/checkm_data
[2023-03-18 08:43:05,975] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:43:05,981] [INFO] Task started: CheckM
[2023-03-18 08:43:05,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26696/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26696/checkm_input OceanDNA-b26696/checkm_result
[2023-03-18 08:43:56,969] [INFO] Task succeeded: CheckM
[2023-03-18 08:43:56,969] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 08:43:57,005] [INFO] ===== Completeness check finished =====
[2023-03-18 08:43:57,005] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:43:57,005] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26696/markers.fasta)
[2023-03-18 08:43:57,006] [INFO] Task started: Blastn
[2023-03-18 08:43:57,006] [INFO] Running command: blastn -query OceanDNA-b26696/markers.fasta -db /var/lib/cwl/stg1eb708ba-3d79-4a06-a57b-9faef2397289/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26696/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:43:58,029] [INFO] Task succeeded: Blastn
[2023-03-18 08:43:58,033] [INFO] Selected 12 target genomes.
[2023-03-18 08:43:58,033] [INFO] Target genome list was writen to OceanDNA-b26696/target_genomes_gtdb.txt
[2023-03-18 08:43:58,045] [INFO] Task started: fastANI
[2023-03-18 08:43:58,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg426acf0b-1e01-4a5a-a939-f2c4cc9d723c/OceanDNA-b26696.fa --refList OceanDNA-b26696/target_genomes_gtdb.txt --output OceanDNA-b26696/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:44:07,522] [INFO] Task succeeded: fastANI
[2023-03-18 08:44:07,530] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:44:07,530] [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_009758415.1	s__Devosia marina	87.8568	841	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	97.05	97.05	0.85	0.85	2	-
GCF_014197055.1	s__Devosia subaequoris	86.376	828	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056405.1	s__Devosia indica	85.6102	794	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016411825.1	s__Devosia sp016411825	81.5829	683	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650025.1	s__Devosia elaeis	81.2338	615	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900631955.1	s__Devosia sp001899045	80.4971	549	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	98.09	98.08	0.92	0.92	4	-
GCF_900177655.1	s__Devosia lucknowensis	80.4167	607	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969445.1	s__Devosia chinhatensis	80.1292	544	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743575.1	s__Devosia riboflavina	79.7466	533	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427605.1	s__Devosia sp001427605	79.6861	538	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307565.1	s__Devosia sp017307565	79.3145	435	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002375765.1	s__Pelagibacterium sp002375765	77.29	210	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.84	99.84	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-03-18 08:44:07,533] [INFO] GTDB search result was written to OceanDNA-b26696/result_gtdb.tsv
[2023-03-18 08:44:07,544] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:44:07,551] [INFO] DFAST_QC result json was written to OceanDNA-b26696/dqc_result.json
[2023-03-18 08:44:07,551] [INFO] DFAST_QC completed!
[2023-03-18 08:44:07,551] [INFO] Total running time: 0h1m33s