[2023-03-16 07:09:52,126] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:09:52,126] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:09:52,126] [INFO] DQC Reference Directory: /var/lib/cwl/stge237f3f2-50c4-4d89-8e1c-a0cd6074f154/dqc_reference
[2023-03-16 07:09:56,340] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:09:56,341] [INFO] Task started: Prodigal
[2023-03-16 07:09:56,341] [INFO] Running command: cat /var/lib/cwl/stgb5da003e-228a-4ed8-ac47-dee94a1f2241/OceanDNA-b4252.fa | prodigal -d OceanDNA-b4252/cds.fna -a OceanDNA-b4252/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:10:20,635] [INFO] Task succeeded: Prodigal
[2023-03-16 07:10:20,635] [INFO] Task started: HMMsearch
[2023-03-16 07:10:20,635] [INFO] Running command: hmmsearch --tblout OceanDNA-b4252/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge237f3f2-50c4-4d89-8e1c-a0cd6074f154/dqc_reference/reference_markers.hmm OceanDNA-b4252/protein.faa > /dev/null
[2023-03-16 07:10:20,812] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:10:20,812] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb5da003e-228a-4ed8-ac47-dee94a1f2241/OceanDNA-b4252.fa]
[2023-03-16 07:10:20,834] [INFO] Query marker FASTA was written to OceanDNA-b4252/markers.fasta
[2023-03-16 07:10:20,835] [INFO] Task started: Blastn
[2023-03-16 07:10:20,836] [INFO] Running command: blastn -query OceanDNA-b4252/markers.fasta -db /var/lib/cwl/stge237f3f2-50c4-4d89-8e1c-a0cd6074f154/dqc_reference/reference_markers.fasta -out OceanDNA-b4252/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:10:21,418] [INFO] Task succeeded: Blastn
[2023-03-16 07:10:21,419] [INFO] Selected 15 target genomes.
[2023-03-16 07:10:21,419] [INFO] Target genome list was writen to OceanDNA-b4252/target_genomes.txt
[2023-03-16 07:10:21,431] [INFO] Task started: fastANI
[2023-03-16 07:10:21,431] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5da003e-228a-4ed8-ac47-dee94a1f2241/OceanDNA-b4252.fa --refList OceanDNA-b4252/target_genomes.txt --output OceanDNA-b4252/fastani_result.tsv --threads 1
[2023-03-16 07:10:35,669] [INFO] Task succeeded: fastANI
[2023-03-16 07:10:35,669] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge237f3f2-50c4-4d89-8e1c-a0cd6074f154/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:10:35,670] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge237f3f2-50c4-4d89-8e1c-a0cd6074f154/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:10:35,679] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:10:35,679] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:10:35,680] [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
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	81.5475	582	808	95	below_threshold
Hymenobacter ruricola	strain=BT662	GCA_015694525.1	2791023	2791023	type	True	81.4274	593	808	95	below_threshold
Hymenobacter caeli	strain=9A	GCA_013294115.1	2735894	2735894	type	True	81.1808	534	808	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	81.0445	553	808	95	below_threshold
Hymenobacter properus	strain=BT439	GCA_015694735.1	2791026	2791026	type	True	81.0362	562	808	95	below_threshold
Hymenobacter rubidus	strain=DG7B	GCA_016734815.1	1441626	1441626	type	True	80.8502	538	808	95	below_threshold
Hymenobacter coccineus	strain=CCM 8649	GCA_001816125.1	1908235	1908235	type	True	80.679	489	808	95	below_threshold
Hymenobacter glacialis	strain=CCM 8648	GCA_001816165.1	1908236	1908236	type	True	80.6337	470	808	95	below_threshold
Hymenobacter sedentarius	strain=DG5B	GCA_001507645.1	1411621	1411621	type	True	80.6276	503	808	95	below_threshold
Hymenobacter lapidarius	strain=CCM 8643	GCA_001816145.1	1908237	1908237	type	True	80.6222	490	808	95	below_threshold
Hymenobacter nivis	strain=NBRC 111535	GCA_003149515.1	1850093	1850093	type	True	80.4294	494	808	95	below_threshold
Hymenobacter polaris	strain=RP-2-7	GCA_012927305.1	2682546	2682546	type	True	79.8383	455	808	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	79.7172	427	808	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	79.6536	434	808	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	78.637	407	808	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:10:35,680] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4252/tc_result.tsv
[2023-03-16 07:10:35,681] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:10:35,681] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:10:35,681] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge237f3f2-50c4-4d89-8e1c-a0cd6074f154/dqc_reference/checkm_data
[2023-03-16 07:10:35,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:10:35,753] [INFO] Task started: CheckM
[2023-03-16 07:10:35,753] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4252/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4252/checkm_input OceanDNA-b4252/checkm_result
[2023-03-16 07:11:35,234] [INFO] Task succeeded: CheckM
[2023-03-16 07:11:35,234] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.49%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 07:11:35,239] [INFO] ===== Completeness check finished =====
[2023-03-16 07:11:35,239] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:11:35,239] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4252/markers.fasta)
[2023-03-16 07:11:35,240] [INFO] Task started: Blastn
[2023-03-16 07:11:35,240] [INFO] Running command: blastn -query OceanDNA-b4252/markers.fasta -db /var/lib/cwl/stge237f3f2-50c4-4d89-8e1c-a0cd6074f154/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4252/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:11:36,013] [INFO] Task succeeded: Blastn
[2023-03-16 07:11:36,015] [INFO] Selected 15 target genomes.
[2023-03-16 07:11:36,015] [INFO] Target genome list was writen to OceanDNA-b4252/target_genomes_gtdb.txt
[2023-03-16 07:11:36,031] [INFO] Task started: fastANI
[2023-03-16 07:11:36,031] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5da003e-228a-4ed8-ac47-dee94a1f2241/OceanDNA-b4252.fa --refList OceanDNA-b4252/target_genomes_gtdb.txt --output OceanDNA-b4252/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:11:50,193] [INFO] Task succeeded: fastANI
[2023-03-16 07:11:50,202] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:11:50,202] [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_016427455.1	s__Hymenobacter sp016427455	81.5113	579	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	95.46	95.46	0.89	0.89	2	-
GCF_013294115.1	s__Hymenobacter caeli	81.248	529	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694735.1	s__Hymenobacter properus	81.0209	563	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012275535.1	s__Hymenobacter artigasi	81.0151	557	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439025.1	s__Hymenobacter nivis_A	80.9918	512	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016056375.1	s__Hymenobacter negativus_A	80.9216	538	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.78	97.78	0.95	0.95	3	-
GCF_018967845.1	s__Hymenobacter sp018967845	80.8664	517	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	99.02	98.98	0.94	0.93	3	-
GCF_001816125.1	s__Hymenobacter coccineus	80.6857	488	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507645.1	s__Hymenobacter sedentarius	80.6514	501	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001816145.1	s__Hymenobacter lapidarius	80.6222	490	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001816165.1	s__Hymenobacter glacialis	80.6207	471	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000715495.1	s__Hymenobacter sp000715495	80.4568	502	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149515.1	s__Hymenobacter nivis	80.4533	492	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927305.1	s__Hymenobacter polaris	79.8714	453	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001596155.1	s__Hymenobacter sp001596155	79.505	434	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:11:50,202] [INFO] GTDB search result was written to OceanDNA-b4252/result_gtdb.tsv
[2023-03-16 07:11:50,203] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:11:50,205] [INFO] DFAST_QC result json was written to OceanDNA-b4252/dqc_result.json
[2023-03-16 07:11:50,205] [INFO] DFAST_QC completed!
[2023-03-16 07:11:50,205] [INFO] Total running time: 0h1m58s