[2023-03-17 02:49:37,510] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:49:37,510] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:49:37,510] [INFO] DQC Reference Directory: /var/lib/cwl/stgaab4484f-428f-49bf-97ba-6caabff8ebeb/dqc_reference
[2023-03-17 02:49:38,635] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:49:38,635] [INFO] Task started: Prodigal
[2023-03-17 02:49:38,635] [INFO] Running command: cat /var/lib/cwl/stg45436c20-c243-4966-88be-9a2219cb4242/OceanDNA-b7209.fa | prodigal -d OceanDNA-b7209/cds.fna -a OceanDNA-b7209/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:49:52,106] [INFO] Task succeeded: Prodigal
[2023-03-17 02:49:52,106] [INFO] Task started: HMMsearch
[2023-03-17 02:49:52,106] [INFO] Running command: hmmsearch --tblout OceanDNA-b7209/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaab4484f-428f-49bf-97ba-6caabff8ebeb/dqc_reference/reference_markers.hmm OceanDNA-b7209/protein.faa > /dev/null
[2023-03-17 02:49:52,336] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:49:52,337] [INFO] Found 6/6 markers.
[2023-03-17 02:49:52,354] [INFO] Query marker FASTA was written to OceanDNA-b7209/markers.fasta
[2023-03-17 02:49:52,356] [INFO] Task started: Blastn
[2023-03-17 02:49:52,356] [INFO] Running command: blastn -query OceanDNA-b7209/markers.fasta -db /var/lib/cwl/stgaab4484f-428f-49bf-97ba-6caabff8ebeb/dqc_reference/reference_markers.fasta -out OceanDNA-b7209/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:49:52,919] [INFO] Task succeeded: Blastn
[2023-03-17 02:49:52,920] [INFO] Selected 16 target genomes.
[2023-03-17 02:49:52,920] [INFO] Target genome list was writen to OceanDNA-b7209/target_genomes.txt
[2023-03-17 02:49:53,040] [INFO] Task started: fastANI
[2023-03-17 02:49:53,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg45436c20-c243-4966-88be-9a2219cb4242/OceanDNA-b7209.fa --refList OceanDNA-b7209/target_genomes.txt --output OceanDNA-b7209/fastani_result.tsv --threads 1
[2023-03-17 02:50:02,523] [INFO] Task succeeded: fastANI
[2023-03-17 02:50:02,523] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaab4484f-428f-49bf-97ba-6caabff8ebeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:50:02,523] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaab4484f-428f-49bf-97ba-6caabff8ebeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:50:02,532] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:50:02,532] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 02:50:02,532] [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
Gramella portivictoriae	strain=DSM 23547	GCA_000423045.1	326069	326069	type	True	85.6769	502	569	95	below_threshold
Gramella gaetbulicola	strain=DSM 23082	GCA_003054225.1	703340	703340	type	True	78.7672	214	569	95	below_threshold
Gramella echinicola	strain=DSM 19838	GCA_000423065.1	279359	279359	type	True	78.6755	227	569	95	below_threshold
Gramella forsetii	strain=KT0803	GCA_000060345.1	411153	411153	type	True	78.5813	202	569	95	below_threshold
Gramella forsetii	strain=CGMCC 1.15422	GCA_014642775.1	411153	411153	type	True	78.5527	210	569	95	below_threshold
Gramella sabulilitoris	strain=HSMS-1	GCA_007050985.1	2583991	2583991	type	True	78.3316	195	569	95	below_threshold
Gramella aestuarii	strain=BS12	GCA_009735585.1	1028746	1028746	type	True	78.323	187	569	95	below_threshold
Gramella lutea	strain=YJ019	GCA_022489035.1	1607951	1607951	type	True	78.1785	202	569	95	below_threshold
Gramella crocea	strain=YB25	GCA_022410465.1	2904124	2904124	type	True	78.1035	157	569	95	below_threshold
Gramella salexigens	strain=LPB0144	GCA_001889005.1	1913577	1913577	type	True	77.6217	154	569	95	below_threshold
Zunongwangia atlantica	strain=22II14-10F7	GCA_002094855.1	1502297	1502297	type	True	76.8047	102	569	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	76.6651	94	569	95	below_threshold
Gillisia hiemivivida	strain=IC154	GCA_007997295.1	291190	291190	type	True	76.4095	63	569	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:50:02,532] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7209/tc_result.tsv
[2023-03-17 02:50:02,532] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:50:02,533] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:50:02,533] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaab4484f-428f-49bf-97ba-6caabff8ebeb/dqc_reference/checkm_data
[2023-03-17 02:50:02,533] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:50:02,538] [INFO] Task started: CheckM
[2023-03-17 02:50:02,538] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7209/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7209/checkm_input OceanDNA-b7209/checkm_result
[2023-03-17 02:50:40,762] [INFO] Task succeeded: CheckM
[2023-03-17 02:50:40,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 12.50%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 02:50:40,839] [INFO] ===== Completeness check finished =====
[2023-03-17 02:50:40,839] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:50:40,839] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7209/markers.fasta)
[2023-03-17 02:50:40,841] [INFO] Task started: Blastn
[2023-03-17 02:50:40,841] [INFO] Running command: blastn -query OceanDNA-b7209/markers.fasta -db /var/lib/cwl/stgaab4484f-428f-49bf-97ba-6caabff8ebeb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7209/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:50:41,589] [INFO] Task succeeded: Blastn
[2023-03-17 02:50:41,593] [INFO] Selected 11 target genomes.
[2023-03-17 02:50:41,593] [INFO] Target genome list was writen to OceanDNA-b7209/target_genomes_gtdb.txt
[2023-03-17 02:50:41,600] [INFO] Task started: fastANI
[2023-03-17 02:50:41,600] [INFO] Running command: fastANI --query /var/lib/cwl/stg45436c20-c243-4966-88be-9a2219cb4242/OceanDNA-b7209.fa --refList OceanDNA-b7209/target_genomes_gtdb.txt --output OceanDNA-b7209/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:50:48,012] [INFO] Task succeeded: fastANI
[2023-03-17 02:50:48,019] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:50:48,019] [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_006714895.1	s__Gramella sp006714895	92.5514	518	569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423045.1	s__Gramella portivictoriae	85.6769	502	569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054225.1	s__Gramella gaetbulicola	78.7672	214	569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423065.1	s__Gramella echinicola	78.6755	227	569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	97.44	97.44	0.87	0.87	2	-
GCF_900105135.1	s__Gramella sp900105135	78.6323	213	569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000060345.1	s__Gramella forsetii	78.5813	202	569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007050985.1	s__Gramella sabulilitoris	78.3316	195	569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009735585.1	s__Gramella aestuarii	78.323	187	569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004332155.1	s__Gramella sp004332155	77.7745	135	569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113135.1	s__Salegentibacter agarivorans	76.8059	101	569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	97.64	95.65	0.87	0.86	4	-
GCF_007997295.1	s__Gillisia hiemivivida	76.4095	63	569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	95.35	95.35	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-03-17 02:50:48,021] [INFO] GTDB search result was written to OceanDNA-b7209/result_gtdb.tsv
[2023-03-17 02:50:48,023] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:50:48,026] [INFO] DFAST_QC result json was written to OceanDNA-b7209/dqc_result.json
[2023-03-17 02:50:48,026] [INFO] DFAST_QC completed!
[2023-03-17 02:50:48,026] [INFO] Total running time: 0h1m11s