[2023-03-18 00:05:54,480] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:05:54,480] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:05:54,480] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d2a95fd-caf9-4fe0-ba53-74d1a876891a/dqc_reference
[2023-03-18 00:05:55,692] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:05:55,693] [INFO] Task started: Prodigal
[2023-03-18 00:05:55,693] [INFO] Running command: cat /var/lib/cwl/stgdab35437-f956-4981-bb3d-16ae910e981b/OceanDNA-b9637.fa | prodigal -d OceanDNA-b9637/cds.fna -a OceanDNA-b9637/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:06:19,646] [INFO] Task succeeded: Prodigal
[2023-03-18 00:06:19,647] [INFO] Task started: HMMsearch
[2023-03-18 00:06:19,647] [INFO] Running command: hmmsearch --tblout OceanDNA-b9637/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d2a95fd-caf9-4fe0-ba53-74d1a876891a/dqc_reference/reference_markers.hmm OceanDNA-b9637/protein.faa > /dev/null
[2023-03-18 00:06:19,875] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:06:19,875] [INFO] Found 6/6 markers.
[2023-03-18 00:06:19,898] [INFO] Query marker FASTA was written to OceanDNA-b9637/markers.fasta
[2023-03-18 00:06:19,899] [INFO] Task started: Blastn
[2023-03-18 00:06:19,899] [INFO] Running command: blastn -query OceanDNA-b9637/markers.fasta -db /var/lib/cwl/stg9d2a95fd-caf9-4fe0-ba53-74d1a876891a/dqc_reference/reference_markers.fasta -out OceanDNA-b9637/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:06:20,477] [INFO] Task succeeded: Blastn
[2023-03-18 00:06:20,478] [INFO] Selected 15 target genomes.
[2023-03-18 00:06:20,478] [INFO] Target genome list was writen to OceanDNA-b9637/target_genomes.txt
[2023-03-18 00:06:20,486] [INFO] Task started: fastANI
[2023-03-18 00:06:20,486] [INFO] Running command: fastANI --query /var/lib/cwl/stgdab35437-f956-4981-bb3d-16ae910e981b/OceanDNA-b9637.fa --refList OceanDNA-b9637/target_genomes.txt --output OceanDNA-b9637/fastani_result.tsv --threads 1
[2023-03-18 00:06:32,356] [INFO] Task succeeded: fastANI
[2023-03-18 00:06:32,356] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d2a95fd-caf9-4fe0-ba53-74d1a876891a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:06:32,357] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d2a95fd-caf9-4fe0-ba53-74d1a876891a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:06:32,365] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:06:32,365] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:06:32,366] [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 arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	89.643	1021	1233	95	below_threshold
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	87.1408	970	1233	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	80.5754	726	1233	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	80.4985	692	1233	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	80.3325	734	1233	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	80.3309	742	1233	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	80.2295	662	1233	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	80.1209	678	1233	95	below_threshold
Maribacter forsetii	strain=DSM 18668	GCA_000744105.1	444515	444515	type	True	79.8363	626	1233	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	79.4263	580	1233	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	77.1463	238	1233	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	76.326	51	1233	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	75.622	73	1233	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:06:32,367] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9637/tc_result.tsv
[2023-03-18 00:06:32,367] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:06:32,367] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:06:32,367] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d2a95fd-caf9-4fe0-ba53-74d1a876891a/dqc_reference/checkm_data
[2023-03-18 00:06:32,368] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:06:32,396] [INFO] Task started: CheckM
[2023-03-18 00:06:32,396] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9637/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9637/checkm_input OceanDNA-b9637/checkm_result
[2023-03-18 00:07:31,560] [INFO] Task succeeded: CheckM
[2023-03-18 00:07:31,561] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:07:31,582] [INFO] ===== Completeness check finished =====
[2023-03-18 00:07:31,582] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:07:31,582] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9637/markers.fasta)
[2023-03-18 00:07:31,583] [INFO] Task started: Blastn
[2023-03-18 00:07:31,583] [INFO] Running command: blastn -query OceanDNA-b9637/markers.fasta -db /var/lib/cwl/stg9d2a95fd-caf9-4fe0-ba53-74d1a876891a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9637/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:07:32,439] [INFO] Task succeeded: Blastn
[2023-03-18 00:07:32,440] [INFO] Selected 11 target genomes.
[2023-03-18 00:07:32,440] [INFO] Target genome list was writen to OceanDNA-b9637/target_genomes_gtdb.txt
[2023-03-18 00:07:32,450] [INFO] Task started: fastANI
[2023-03-18 00:07:32,450] [INFO] Running command: fastANI --query /var/lib/cwl/stgdab35437-f956-4981-bb3d-16ae910e981b/OceanDNA-b9637.fa --refList OceanDNA-b9637/target_genomes_gtdb.txt --output OceanDNA-b9637/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:07:42,090] [INFO] Task succeeded: fastANI
[2023-03-18 00:07:42,097] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:07:42,097] [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_900167935.1	s__Maribacter arcticus	89.643	1021	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109345.1	s__Maribacter orientalis	87.1337	971	1233	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	80.9119	739	1233	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	80.5754	726	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCF_900142175.1	s__Maribacter aquivivus	80.4898	693	1233	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	80.431	709	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001913155.1	s__Maribacter hydrothermalis	80.3325	734	1233	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	80.2207	663	1233	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	80.1308	676	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744105.1	s__Maribacter forsetii	79.8363	626	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971785.1	s__Seonamhaeicola sp001971785	76.3295	89	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:07:42,101] [INFO] GTDB search result was written to OceanDNA-b9637/result_gtdb.tsv
[2023-03-18 00:07:42,101] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:07:42,105] [INFO] DFAST_QC result json was written to OceanDNA-b9637/dqc_result.json
[2023-03-18 00:07:42,105] [INFO] DFAST_QC completed!
[2023-03-18 00:07:42,105] [INFO] Total running time: 0h1m48s