[2023-03-17 03:28:37,120] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:28:37,120] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:28:37,120] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bd2fe50-e8c3-4911-abba-b6c9c7041ffe/dqc_reference
[2023-03-17 03:28:38,235] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:28:38,236] [INFO] Task started: Prodigal
[2023-03-17 03:28:38,236] [INFO] Running command: cat /var/lib/cwl/stg01f1a411-514b-4e9d-a3d2-a80fd3c25512/OceanDNA-b9746.fa | prodigal -d OceanDNA-b9746/cds.fna -a OceanDNA-b9746/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:29:01,877] [INFO] Task succeeded: Prodigal
[2023-03-17 03:29:01,877] [INFO] Task started: HMMsearch
[2023-03-17 03:29:01,878] [INFO] Running command: hmmsearch --tblout OceanDNA-b9746/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bd2fe50-e8c3-4911-abba-b6c9c7041ffe/dqc_reference/reference_markers.hmm OceanDNA-b9746/protein.faa > /dev/null
[2023-03-17 03:29:02,105] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:29:02,105] [INFO] Found 6/6 markers.
[2023-03-17 03:29:02,128] [INFO] Query marker FASTA was written to OceanDNA-b9746/markers.fasta
[2023-03-17 03:29:02,129] [INFO] Task started: Blastn
[2023-03-17 03:29:02,129] [INFO] Running command: blastn -query OceanDNA-b9746/markers.fasta -db /var/lib/cwl/stg4bd2fe50-e8c3-4911-abba-b6c9c7041ffe/dqc_reference/reference_markers.fasta -out OceanDNA-b9746/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:29:02,724] [INFO] Task succeeded: Blastn
[2023-03-17 03:29:02,725] [INFO] Selected 16 target genomes.
[2023-03-17 03:29:02,725] [INFO] Target genome list was writen to OceanDNA-b9746/target_genomes.txt
[2023-03-17 03:29:02,731] [INFO] Task started: fastANI
[2023-03-17 03:29:02,731] [INFO] Running command: fastANI --query /var/lib/cwl/stg01f1a411-514b-4e9d-a3d2-a80fd3c25512/OceanDNA-b9746.fa --refList OceanDNA-b9746/target_genomes.txt --output OceanDNA-b9746/fastani_result.tsv --threads 1
[2023-03-17 03:29:12,771] [INFO] Task succeeded: fastANI
[2023-03-17 03:29:12,771] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bd2fe50-e8c3-4911-abba-b6c9c7041ffe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:29:12,771] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bd2fe50-e8c3-4911-abba-b6c9c7041ffe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:29:12,780] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 03:29:12,780] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 03:29:12,780] [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
Mesonia oceanica	strain=ISS653	GCA_902499555.1	2687242	2687242	type	True	99.9744	1244	1252	95	conclusive
Mesonia mobilis	strain=KCTC 12708	GCA_014651475.1	369791	369791	type	True	81.1516	667	1252	95	below_threshold
Mesonia mobilis	strain=DSM 19841	GCA_000423405.1	369791	369791	type	True	81.1426	670	1252	95	below_threshold
Mesonia phycicola	strain=DSM 21425	GCA_900141885.1	579105	579105	type	True	78.9455	462	1252	95	below_threshold
Zunongwangia profunda	strain=SMA-87	GCA_000023465.1	398743	398743	type	True	78.6523	202	1252	95	below_threshold
Mesonia algae	strain=DSM 15361	GCA_003253545.1	213248	213248	type	True	77.4544	254	1252	95	below_threshold
Zunongwangia atlantica	strain=22II14-10F7	GCA_002094855.1	1502297	1502297	type	True	77.2745	201	1252	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	76.751	91	1252	95	below_threshold
Pustulibacterium marinum	strain=CGMCC 1.12333	GCA_900116665.1	1224947	1224947	type	True	76.4188	101	1252	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.1905	80	1252	95	below_threshold
Gramella lutea	strain=YJ019	GCA_022489035.1	1607951	1607951	type	True	76.0089	80	1252	95	below_threshold
Kordia algicida	strain=OT-1	GCA_000154725.1	221066	221066	type	True	75.6781	106	1252	95	below_threshold
Tenacibaculum adriaticum	strain=DSM 18961	GCA_008124875.1	413713	413713	type	True	75.6695	79	1252	95	below_threshold
Mesohalobacter halotolerans	strain=WDS2C27	GCA_006120725.1	1883405	1883405	type	True	75.5504	55	1252	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:29:12,780] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9746/tc_result.tsv
[2023-03-17 03:29:12,781] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:29:12,781] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:29:12,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bd2fe50-e8c3-4911-abba-b6c9c7041ffe/dqc_reference/checkm_data
[2023-03-17 03:29:12,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:29:12,786] [INFO] Task started: CheckM
[2023-03-17 03:29:12,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9746/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9746/checkm_input OceanDNA-b9746/checkm_result
[2023-03-17 03:30:11,618] [INFO] Task succeeded: CheckM
[2023-03-17 03:30:11,618] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:30:11,621] [INFO] ===== Completeness check finished =====
[2023-03-17 03:30:11,621] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:30:11,621] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9746/markers.fasta)
[2023-03-17 03:30:11,621] [INFO] Task started: Blastn
[2023-03-17 03:30:11,621] [INFO] Running command: blastn -query OceanDNA-b9746/markers.fasta -db /var/lib/cwl/stg4bd2fe50-e8c3-4911-abba-b6c9c7041ffe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9746/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:30:12,455] [INFO] Task succeeded: Blastn
[2023-03-17 03:30:12,456] [INFO] Selected 7 target genomes.
[2023-03-17 03:30:12,456] [INFO] Target genome list was writen to OceanDNA-b9746/target_genomes_gtdb.txt
[2023-03-17 03:30:12,463] [INFO] Task started: fastANI
[2023-03-17 03:30:12,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg01f1a411-514b-4e9d-a3d2-a80fd3c25512/OceanDNA-b9746.fa --refList OceanDNA-b9746/target_genomes_gtdb.txt --output OceanDNA-b9746/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:30:17,614] [INFO] Task succeeded: fastANI
[2023-03-17 03:30:17,619] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 03:30:17,619] [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_902499555.1	s__Mesonia oceanica	99.9744	1244	1252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.91	99.87	0.96	0.92	8	conclusive
GCF_008692195.1	s__Mesonia sp008692195	85.1707	882	1252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423405.1	s__Mesonia mobilis	81.1327	671	1252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
GCA_012964435.1	s__Mesonia sp012964435	80.8289	616	1252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900141885.1	s__Mesonia phycicola	78.9502	462	1252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667275.1	s__Mesonia aquimarina	78.0235	334	1252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002631855.1	s__Marixanthomonas sp002631855	76.3932	122	1252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:30:17,619] [INFO] GTDB search result was written to OceanDNA-b9746/result_gtdb.tsv
[2023-03-17 03:30:17,619] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:30:17,621] [INFO] DFAST_QC result json was written to OceanDNA-b9746/dqc_result.json
[2023-03-17 03:30:17,621] [INFO] DFAST_QC completed!
[2023-03-17 03:30:17,621] [INFO] Total running time: 0h1m41s