[2023-03-15 22:44:22,022] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:44:22,022] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:44:22,023] [INFO] DQC Reference Directory: /var/lib/cwl/stg30f066a0-e5bc-42db-98e7-ce9492f817fb/dqc_reference
[2023-03-15 22:44:23,186] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:44:23,187] [INFO] Task started: Prodigal
[2023-03-15 22:44:23,187] [INFO] Running command: cat /var/lib/cwl/stg958c73ef-7bcc-472d-8831-f366f43ca2d4/OceanDNA-b6753.fa | prodigal -d OceanDNA-b6753/cds.fna -a OceanDNA-b6753/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:44:42,380] [INFO] Task succeeded: Prodigal
[2023-03-15 22:44:42,381] [INFO] Task started: HMMsearch
[2023-03-15 22:44:42,381] [INFO] Running command: hmmsearch --tblout OceanDNA-b6753/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30f066a0-e5bc-42db-98e7-ce9492f817fb/dqc_reference/reference_markers.hmm OceanDNA-b6753/protein.faa > /dev/null
[2023-03-15 22:44:42,583] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:44:42,584] [INFO] Found 6/6 markers.
[2023-03-15 22:44:42,633] [INFO] Query marker FASTA was written to OceanDNA-b6753/markers.fasta
[2023-03-15 22:44:42,634] [INFO] Task started: Blastn
[2023-03-15 22:44:42,634] [INFO] Running command: blastn -query OceanDNA-b6753/markers.fasta -db /var/lib/cwl/stg30f066a0-e5bc-42db-98e7-ce9492f817fb/dqc_reference/reference_markers.fasta -out OceanDNA-b6753/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:44:43,265] [INFO] Task succeeded: Blastn
[2023-03-15 22:44:43,272] [INFO] Selected 20 target genomes.
[2023-03-15 22:44:43,273] [INFO] Target genome list was writen to OceanDNA-b6753/target_genomes.txt
[2023-03-15 22:44:43,282] [INFO] Task started: fastANI
[2023-03-15 22:44:43,282] [INFO] Running command: fastANI --query /var/lib/cwl/stg958c73ef-7bcc-472d-8831-f366f43ca2d4/OceanDNA-b6753.fa --refList OceanDNA-b6753/target_genomes.txt --output OceanDNA-b6753/fastani_result.tsv --threads 1
[2023-03-15 22:44:57,025] [INFO] Task succeeded: fastANI
[2023-03-15 22:44:57,025] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30f066a0-e5bc-42db-98e7-ce9492f817fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:44:57,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30f066a0-e5bc-42db-98e7-ce9492f817fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:44:57,037] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:44:57,037] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 22:44:57,037] [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
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	79.399	488	1042	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	79.2721	459	1042	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	79.2561	460	1042	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	79.2377	457	1042	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	79.2236	461	1042	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	79.1937	467	1042	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	78.8927	454	1042	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	78.633	418	1042	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	78.6302	451	1042	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	78.5396	439	1042	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	78.4647	408	1042	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	78.3465	389	1042	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	78.1806	361	1042	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	77.9186	368	1042	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.6724	345	1042	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	77.3876	251	1042	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.3625	244	1042	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	77.1905	225	1042	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.0971	235	1042	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.7009	171	1042	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:44:57,040] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6753/tc_result.tsv
[2023-03-15 22:44:57,043] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:44:57,043] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:44:57,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30f066a0-e5bc-42db-98e7-ce9492f817fb/dqc_reference/checkm_data
[2023-03-15 22:44:57,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:44:57,127] [INFO] Task started: CheckM
[2023-03-15 22:44:57,128] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6753/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6753/checkm_input OceanDNA-b6753/checkm_result
[2023-03-15 22:45:46,368] [INFO] Task succeeded: CheckM
[2023-03-15 22:45:46,368] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:45:46,628] [INFO] ===== Completeness check finished =====
[2023-03-15 22:45:46,628] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:45:46,628] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6753/markers.fasta)
[2023-03-15 22:45:46,629] [INFO] Task started: Blastn
[2023-03-15 22:45:46,629] [INFO] Running command: blastn -query OceanDNA-b6753/markers.fasta -db /var/lib/cwl/stg30f066a0-e5bc-42db-98e7-ce9492f817fb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6753/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:45:47,548] [INFO] Task succeeded: Blastn
[2023-03-15 22:45:47,556] [INFO] Selected 15 target genomes.
[2023-03-15 22:45:47,556] [INFO] Target genome list was writen to OceanDNA-b6753/target_genomes_gtdb.txt
[2023-03-15 22:45:47,628] [INFO] Task started: fastANI
[2023-03-15 22:45:47,628] [INFO] Running command: fastANI --query /var/lib/cwl/stg958c73ef-7bcc-472d-8831-f366f43ca2d4/OceanDNA-b6753.fa --refList OceanDNA-b6753/target_genomes_gtdb.txt --output OceanDNA-b6753/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:45:58,147] [INFO] Task succeeded: fastANI
[2023-03-15 22:45:58,156] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:45:58,156] [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_900114265.1	s__Flaviramulus basaltis	79.9614	556	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	79.4576	504	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	79.4189	486	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001275.1	s__Flaviramulus sp013001275	79.3042	394	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	79.2395	459	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014202225.1	s__Algibacter_B amylolyticus	79.2274	459	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCA_905480415.1	s__Algibacter_B sp905480415	79.2172	441	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112595.1	s__Algibacter_B pectinivorans	78.8927	454	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	78.795	453	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	78.7261	434	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	78.6208	452	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341235.1	s__Mariniflexile fucanivorans	78.5486	438	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971785.1	s__Seonamhaeicola sp001971785	78.2611	424	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002886045.1	s__Flavivirga eckloniae	78.1194	373	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259525.1	s__Olleya aquimaris	77.3982	250	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:45:58,174] [INFO] GTDB search result was written to OceanDNA-b6753/result_gtdb.tsv
[2023-03-15 22:45:58,210] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:45:58,226] [INFO] DFAST_QC result json was written to OceanDNA-b6753/dqc_result.json
[2023-03-15 22:45:58,227] [INFO] DFAST_QC completed!
[2023-03-15 22:45:58,227] [INFO] Total running time: 0h1m36s