[2023-03-16 11:07:23,151] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:07:23,151] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:07:23,151] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c8f015a-eee6-41e8-a55c-f78322ea622f/dqc_reference
[2023-03-16 11:07:24,378] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:07:24,379] [INFO] Task started: Prodigal
[2023-03-16 11:07:24,379] [INFO] Running command: cat /var/lib/cwl/stgde35b67a-2901-43ef-b369-d7c24025bd94/OceanDNA-b36407.fa | prodigal -d OceanDNA-b36407/cds.fna -a OceanDNA-b36407/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:07:47,170] [INFO] Task succeeded: Prodigal
[2023-03-16 11:07:47,171] [INFO] Task started: HMMsearch
[2023-03-16 11:07:47,171] [INFO] Running command: hmmsearch --tblout OceanDNA-b36407/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c8f015a-eee6-41e8-a55c-f78322ea622f/dqc_reference/reference_markers.hmm OceanDNA-b36407/protein.faa > /dev/null
[2023-03-16 11:07:47,420] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:07:47,421] [INFO] Found 6/6 markers.
[2023-03-16 11:07:47,439] [INFO] Query marker FASTA was written to OceanDNA-b36407/markers.fasta
[2023-03-16 11:07:47,441] [INFO] Task started: Blastn
[2023-03-16 11:07:47,441] [INFO] Running command: blastn -query OceanDNA-b36407/markers.fasta -db /var/lib/cwl/stg3c8f015a-eee6-41e8-a55c-f78322ea622f/dqc_reference/reference_markers.fasta -out OceanDNA-b36407/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:07:48,305] [INFO] Task succeeded: Blastn
[2023-03-16 11:07:48,305] [INFO] Selected 13 target genomes.
[2023-03-16 11:07:48,306] [INFO] Target genome list was writen to OceanDNA-b36407/target_genomes.txt
[2023-03-16 11:07:48,311] [INFO] Task started: fastANI
[2023-03-16 11:07:48,311] [INFO] Running command: fastANI --query /var/lib/cwl/stgde35b67a-2901-43ef-b369-d7c24025bd94/OceanDNA-b36407.fa --refList OceanDNA-b36407/target_genomes.txt --output OceanDNA-b36407/fastani_result.tsv --threads 1
[2023-03-16 11:07:57,145] [INFO] Task succeeded: fastANI
[2023-03-16 11:07:57,146] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c8f015a-eee6-41e8-a55c-f78322ea622f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 11:07:57,146] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c8f015a-eee6-41e8-a55c-f78322ea622f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 11:07:57,201] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 11:07:57,202] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 11:07:57,202] [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
Alcanivorax borkumensis	strain=SK2	GCA_000009365.1	59754	59754	type	True	92.835	792	899	95	below_threshold
Alcanivorax jadensis	strain=T9	GCA_000756655.1	64988	64988	type	True	79.7174	516	899	95	below_threshold
Alcanivorax hongdengensis	strain=A-11-3	GCA_000300995.1	519051	519051	type	True	79.5602	427	899	95	below_threshold
Alcanivorax profundi	strain=MTEO17	GCA_003597125.1	2338368	2338368	type	True	79.2813	423	899	95	below_threshold
Alcanivorax sediminis	strain=PA15-N-34	GCA_009601165.1	2663008	2663008	type	True	79.136	396	899	95	below_threshold
Alcanivorax nanhaiticus	strain=19-m-6	GCA_000756665.1	1177154	1177154	type	True	79.0294	410	899	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	77.7674	220	899	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	77.6562	211	899	95	below_threshold
Alcanivorax xenomutans	strain=JC109	GCA_900217905.1	1094342	1094342	type	True	77.1512	209	899	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	77.063	130	899	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 11:07:57,202] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36407/tc_result.tsv
[2023-03-16 11:07:57,202] [INFO] ===== Taxonomy check completed =====
[2023-03-16 11:07:57,202] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:07:57,202] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c8f015a-eee6-41e8-a55c-f78322ea622f/dqc_reference/checkm_data
[2023-03-16 11:07:57,203] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:07:57,207] [INFO] Task started: CheckM
[2023-03-16 11:07:57,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36407/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36407/checkm_input OceanDNA-b36407/checkm_result
[2023-03-16 11:09:02,324] [INFO] Task succeeded: CheckM
[2023-03-16 11:09:02,324] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.06%
Contamintation: 8.71%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 11:09:02,327] [INFO] ===== Completeness check finished =====
[2023-03-16 11:09:02,327] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:09:02,327] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36407/markers.fasta)
[2023-03-16 11:09:02,330] [INFO] Task started: Blastn
[2023-03-16 11:09:02,330] [INFO] Running command: blastn -query OceanDNA-b36407/markers.fasta -db /var/lib/cwl/stg3c8f015a-eee6-41e8-a55c-f78322ea622f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36407/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:09:05,717] [INFO] Task succeeded: Blastn
[2023-03-16 11:09:05,718] [INFO] Selected 10 target genomes.
[2023-03-16 11:09:05,718] [INFO] Target genome list was writen to OceanDNA-b36407/target_genomes_gtdb.txt
[2023-03-16 11:09:05,733] [INFO] Task started: fastANI
[2023-03-16 11:09:05,733] [INFO] Running command: fastANI --query /var/lib/cwl/stgde35b67a-2901-43ef-b369-d7c24025bd94/OceanDNA-b36407.fa --refList OceanDNA-b36407/target_genomes_gtdb.txt --output OceanDNA-b36407/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:09:16,997] [INFO] Task succeeded: fastANI
[2023-03-16 11:09:17,003] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 11:09:17,004] [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_000009365.1	s__Alcanivorax borkumensis	92.8153	793	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.54	99.30	0.96	0.95	6	-
GCF_000155615.1	s__Alcanivorax sp000155615	83.6262	723	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.88	97.69	0.92	0.89	4	-
GCA_002726155.1	s__Alcanivorax sp002726155	83.2418	693	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733835.1	s__Alcanivorax sp002733835	83.1849	698	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107995.1	s__Alcanivorax sp900107995	80.2552	486	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.42	98.03	0.93	0.89	9	-
GCA_003862375.1	s__Alcanivorax jadensis_A	79.8942	487	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.67	99.67	0.92	0.92	2	-
GCF_000756655.1	s__Alcanivorax jadensis	79.7074	517	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.11	97.73	0.92	0.86	7	-
GCA_017794965.1	s__Alcanivorax sp017794965	79.3431	445	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009601165.1	s__Alcanivorax sediminis	79.136	396	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756665.1	s__Alcanivorax nanhaiticus	79.0294	410	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 11:09:17,004] [INFO] GTDB search result was written to OceanDNA-b36407/result_gtdb.tsv
[2023-03-16 11:09:17,004] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:09:17,005] [INFO] DFAST_QC result json was written to OceanDNA-b36407/dqc_result.json
[2023-03-16 11:09:17,005] [INFO] DFAST_QC completed!
[2023-03-16 11:09:17,006] [INFO] Total running time: 0h1m54s