[2023-03-18 07:06:22,011] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:06:22,011] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:06:22,011] [INFO] DQC Reference Directory: /var/lib/cwl/stg23e65365-1456-4eba-a4a7-5e36420701f2/dqc_reference
[2023-03-18 07:06:23,126] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:06:23,126] [INFO] Task started: Prodigal
[2023-03-18 07:06:23,126] [INFO] Running command: cat /var/lib/cwl/stg80d1c967-be55-4c97-9589-ad4f380a5050/OceanDNA-b9646.fa | prodigal -d OceanDNA-b9646/cds.fna -a OceanDNA-b9646/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:06:37,679] [INFO] Task succeeded: Prodigal
[2023-03-18 07:06:37,679] [INFO] Task started: HMMsearch
[2023-03-18 07:06:37,679] [INFO] Running command: hmmsearch --tblout OceanDNA-b9646/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23e65365-1456-4eba-a4a7-5e36420701f2/dqc_reference/reference_markers.hmm OceanDNA-b9646/protein.faa > /dev/null
[2023-03-18 07:06:37,890] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:06:37,891] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg80d1c967-be55-4c97-9589-ad4f380a5050/OceanDNA-b9646.fa]
[2023-03-18 07:06:37,910] [INFO] Query marker FASTA was written to OceanDNA-b9646/markers.fasta
[2023-03-18 07:06:37,911] [INFO] Task started: Blastn
[2023-03-18 07:06:37,911] [INFO] Running command: blastn -query OceanDNA-b9646/markers.fasta -db /var/lib/cwl/stg23e65365-1456-4eba-a4a7-5e36420701f2/dqc_reference/reference_markers.fasta -out OceanDNA-b9646/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:06:38,473] [INFO] Task succeeded: Blastn
[2023-03-18 07:06:38,474] [INFO] Selected 16 target genomes.
[2023-03-18 07:06:38,474] [INFO] Target genome list was writen to OceanDNA-b9646/target_genomes.txt
[2023-03-18 07:06:38,483] [INFO] Task started: fastANI
[2023-03-18 07:06:38,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg80d1c967-be55-4c97-9589-ad4f380a5050/OceanDNA-b9646.fa --refList OceanDNA-b9646/target_genomes.txt --output OceanDNA-b9646/fastani_result.tsv --threads 1
[2023-03-18 07:06:50,443] [INFO] Task succeeded: fastANI
[2023-03-18 07:06:50,443] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23e65365-1456-4eba-a4a7-5e36420701f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:06:50,443] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23e65365-1456-4eba-a4a7-5e36420701f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:06:50,451] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:06:50,451] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:06:50,452] [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
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	92.1288	608	672	95	below_threshold
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	88.4709	590	672	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	80.0465	439	672	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	79.9722	441	672	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	79.9352	433	672	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	79.8778	403	672	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	79.8076	418	672	95	below_threshold
Maribacter ulvicola	strain=DSM 15366	GCA_900155985.1	228959	228959	type	True	79.292	357	672	95	below_threshold
Maribacter dokdonensis	strain=DSW-8	GCA_001447995.1	320912	320912	type	True	79.2255	346	672	95	below_threshold
Maribacter sedimenticola	strain=DSM 19840	GCA_900188415.1	228956	228956	type	True	78.8986	307	672	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	77.2348	123	672	95	below_threshold
Maribacter luteus	strain=RZ05	GCA_009674825.1	2594478	2594478	type	True	76.7786	65	672	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.0977	51	672	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:06:50,452] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9646/tc_result.tsv
[2023-03-18 07:06:50,452] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:06:50,452] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:06:50,452] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23e65365-1456-4eba-a4a7-5e36420701f2/dqc_reference/checkm_data
[2023-03-18 07:06:50,453] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:06:50,457] [INFO] Task started: CheckM
[2023-03-18 07:06:50,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9646/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9646/checkm_input OceanDNA-b9646/checkm_result
[2023-03-18 07:07:29,775] [INFO] Task succeeded: CheckM
[2023-03-18 07:07:29,776] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.47%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:07:29,778] [INFO] ===== Completeness check finished =====
[2023-03-18 07:07:29,778] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:07:29,778] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9646/markers.fasta)
[2023-03-18 07:07:29,778] [INFO] Task started: Blastn
[2023-03-18 07:07:29,779] [INFO] Running command: blastn -query OceanDNA-b9646/markers.fasta -db /var/lib/cwl/stg23e65365-1456-4eba-a4a7-5e36420701f2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9646/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:07:30,516] [INFO] Task succeeded: Blastn
[2023-03-18 07:07:30,517] [INFO] Selected 11 target genomes.
[2023-03-18 07:07:30,517] [INFO] Target genome list was writen to OceanDNA-b9646/target_genomes_gtdb.txt
[2023-03-18 07:07:30,583] [INFO] Task started: fastANI
[2023-03-18 07:07:30,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg80d1c967-be55-4c97-9589-ad4f380a5050/OceanDNA-b9646.fa --refList OceanDNA-b9646/target_genomes_gtdb.txt --output OceanDNA-b9646/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:07:38,719] [INFO] Task succeeded: fastANI
[2023-03-18 07:07:38,726] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:07:38,727] [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_900109345.1	s__Maribacter orientalis	92.1288	608	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167935.1	s__Maribacter arcticus	88.4709	590	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771495.1	s__Maribacter sp005771495	80.5687	441	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050675.1	s__Maribacter sp011050675	80.1006	417	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900112245.1	s__Maribacter stanieri	80.0465	439	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCF_001913155.1	s__Maribacter hydrothermalis	79.9722	441	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004364165.1	s__Maribacter spongiicola	79.8778	403	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364175.1	s__Maribacter caenipelagi	79.8076	418	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447995.1	s__Maribacter dokdonensis	79.2255	346	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.64	97.51	0.89	0.86	13	-
GCF_900188415.1	s__Maribacter sedimenticola	78.8986	307	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.95	97.95	0.90	0.90	2	-
GCF_018100785.1	s__Maribacter sp018100785	77.2266	126	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:07:38,727] [INFO] GTDB search result was written to OceanDNA-b9646/result_gtdb.tsv
[2023-03-18 07:07:38,727] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:07:38,728] [INFO] DFAST_QC result json was written to OceanDNA-b9646/dqc_result.json
[2023-03-18 07:07:38,728] [INFO] DFAST_QC completed!
[2023-03-18 07:07:38,728] [INFO] Total running time: 0h1m17s