[2023-03-16 22:05:57,086] [INFO] DFAST_QC pipeline started.
[2023-03-16 22:05:57,087] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 22:05:57,087] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb715e41-186e-45f8-9453-591cc8ac9d9d/dqc_reference
[2023-03-16 22:05:58,247] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 22:05:58,248] [INFO] Task started: Prodigal
[2023-03-16 22:05:58,248] [INFO] Running command: cat /var/lib/cwl/stgdf2fd973-eb12-4685-bbce-a85ae5003823/OceanDNA-b1733.fa | prodigal -d OceanDNA-b1733/cds.fna -a OceanDNA-b1733/protein.faa -g 11 -q > /dev/null
[2023-03-16 22:06:15,407] [INFO] Task succeeded: Prodigal
[2023-03-16 22:06:15,407] [INFO] Task started: HMMsearch
[2023-03-16 22:06:15,407] [INFO] Running command: hmmsearch --tblout OceanDNA-b1733/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb715e41-186e-45f8-9453-591cc8ac9d9d/dqc_reference/reference_markers.hmm OceanDNA-b1733/protein.faa > /dev/null
[2023-03-16 22:06:15,591] [INFO] Task succeeded: HMMsearch
[2023-03-16 22:06:15,591] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgdf2fd973-eb12-4685-bbce-a85ae5003823/OceanDNA-b1733.fa]
[2023-03-16 22:06:15,617] [INFO] Query marker FASTA was written to OceanDNA-b1733/markers.fasta
[2023-03-16 22:06:15,617] [INFO] Task started: Blastn
[2023-03-16 22:06:15,617] [INFO] Running command: blastn -query OceanDNA-b1733/markers.fasta -db /var/lib/cwl/stgbb715e41-186e-45f8-9453-591cc8ac9d9d/dqc_reference/reference_markers.fasta -out OceanDNA-b1733/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 22:06:16,142] [INFO] Task succeeded: Blastn
[2023-03-16 22:06:16,143] [INFO] Selected 24 target genomes.
[2023-03-16 22:06:16,143] [INFO] Target genome list was writen to OceanDNA-b1733/target_genomes.txt
[2023-03-16 22:06:16,158] [INFO] Task started: fastANI
[2023-03-16 22:06:16,158] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf2fd973-eb12-4685-bbce-a85ae5003823/OceanDNA-b1733.fa --refList OceanDNA-b1733/target_genomes.txt --output OceanDNA-b1733/fastani_result.tsv --threads 1
[2023-03-16 22:06:32,265] [INFO] Task succeeded: fastANI
[2023-03-16 22:06:32,266] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb715e41-186e-45f8-9453-591cc8ac9d9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 22:06:32,266] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb715e41-186e-45f8-9453-591cc8ac9d9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 22:06:32,274] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 22:06:32,275] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 22:06:32,275] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.129	138	876	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	75.6537	118	876	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.2866	137	876	95	below_threshold
Nocardioides nematodiphilus	strain=R-N-C8	GCA_020216525.1	2849669	2849669	type	True	75.1391	60	876	95	below_threshold
Nocardiopsis dassonvillei subsp. crassaminis	strain=D1	GCA_902825375.1	2580523	2014	type	True	74.9815	60	876	95	below_threshold
Rhodococcus pyridinivorans	strain=DSM 44555	GCA_900105195.1	103816	103816	type	True	74.9104	62	876	95	below_threshold
Burkholderia glumae	strain=LMG 2196	GCA_902832765.1	337	337	type	True	74.9061	51	876	95	below_threshold
Burkholderia glumae	strain=ATCC 33617	GCA_000960995.1	337	337	type	True	74.906	51	876	95	below_threshold
Lichenibacterium ramalinae	strain=RmlP001	GCA_004137085.1	2316527	2316527	type	True	74.8694	61	876	95	below_threshold
Nocardiopsis dassonvillei	strain=ATCC 23218	GCA_012396345.1	2014	2014	type	True	74.8462	79	876	95	below_threshold
Nocardiopsis dassonvillei subsp. dassonvillei	strain=DSM 43111	GCA_000092985.1	568208	2014	type	True	74.8401	80	876	95	below_threshold
Nocardiopsis dassonvillei	strain=NCTC10488	GCA_900638215.1	2014	2014	type	True	74.8392	80	876	95	below_threshold
Kineosporia corallincola	strain=J2-2	GCA_018499875.1	2835133	2835133	type	True	74.8014	101	876	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	74.7049	69	876	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 22:06:32,275] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1733/tc_result.tsv
[2023-03-16 22:06:32,275] [INFO] ===== Taxonomy check completed =====
[2023-03-16 22:06:32,275] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 22:06:32,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb715e41-186e-45f8-9453-591cc8ac9d9d/dqc_reference/checkm_data
[2023-03-16 22:06:32,276] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 22:06:32,281] [INFO] Task started: CheckM
[2023-03-16 22:06:32,281] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1733/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1733/checkm_input OceanDNA-b1733/checkm_result
[2023-03-16 22:07:30,060] [INFO] Task succeeded: CheckM
[2023-03-16 22:07:30,061] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.23%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 22:07:30,063] [INFO] ===== Completeness check finished =====
[2023-03-16 22:07:30,063] [INFO] ===== Start GTDB Search =====
[2023-03-16 22:07:30,064] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1733/markers.fasta)
[2023-03-16 22:07:30,065] [INFO] Task started: Blastn
[2023-03-16 22:07:30,065] [INFO] Running command: blastn -query OceanDNA-b1733/markers.fasta -db /var/lib/cwl/stgbb715e41-186e-45f8-9453-591cc8ac9d9d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1733/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 22:07:30,843] [INFO] Task succeeded: Blastn
[2023-03-16 22:07:30,844] [INFO] Selected 20 target genomes.
[2023-03-16 22:07:30,844] [INFO] Target genome list was writen to OceanDNA-b1733/target_genomes_gtdb.txt
[2023-03-16 22:07:31,520] [INFO] Task started: fastANI
[2023-03-16 22:07:31,520] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf2fd973-eb12-4685-bbce-a85ae5003823/OceanDNA-b1733.fa --refList OceanDNA-b1733/target_genomes_gtdb.txt --output OceanDNA-b1733/fastani_result_gtdb.tsv --threads 1
[2023-03-16 22:07:43,104] [INFO] Task succeeded: fastANI
[2023-03-16 22:07:43,113] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 22:07:43,113] [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
GCA_004282895.1	s__SHLQ01 sp004282895	77.3641	174	876	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SHLQ01;g__SHLQ01	95.0	99.55	99.55	0.85	0.85	2	-
GCA_905479685.1	s__SHLQ01 sp905479685	76.5291	93	876	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SHLQ01;g__SHLQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002375.1	s__JABDJW01 sp013002375	76.3257	89	876	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SHLQ01;g__JABDJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002346745.1	s__S20-B6 sp002346745	76.2555	107	876	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	97.72	96.97	0.85	0.81	8	-
GCA_016845305.1	s__UBA9410 sp016845305	76.232	114	876	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903941145.1	s__CAJANQ01 sp903941145	76.0727	61	876	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAJANQ01	95.0	98.35	98.35	0.80	0.80	2	-
GCA_016794585.1	s__JAEUJM01 sp016794585	75.8171	136	876	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAEUJM01;g__JAEUJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969405.1	s__F1-20-MAGs160 sp018969405	75.8143	81	876	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903868545.1	s__CAIPVR01 sp903868545	75.7348	83	876	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAIPVR01	95.0	99.51	99.50	0.87	0.86	3	-
GCA_005888325.1	s__AC-14 sp005888325	75.6226	88	876	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-14;g__AC-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826025.1	s__CADEDH01 sp902826025	75.604	140	876	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SZUA-35;g__CADEDH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903852755.1	s__SXMI01 sp903852755	75.5307	79	876	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	99.71	99.61	0.93	0.92	10	-
GCF_000960995.1	s__Burkholderia glumae	74.9055	51	876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.66	99.30	0.96	0.92	18	-
GCF_003851725.1	s__Cellulomonas algicola	74.8395	73	876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.47	95.68	0.95	0.94	3	-
GCF_004306155.1	s__Cellulomonas biazotea	74.7689	84	876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 22:07:43,113] [INFO] GTDB search result was written to OceanDNA-b1733/result_gtdb.tsv
[2023-03-16 22:07:43,113] [INFO] ===== GTDB Search completed =====
[2023-03-16 22:07:43,115] [INFO] DFAST_QC result json was written to OceanDNA-b1733/dqc_result.json
[2023-03-16 22:07:43,115] [INFO] DFAST_QC completed!
[2023-03-16 22:07:43,115] [INFO] Total running time: 0h1m46s