[2023-03-18 00:53:42,492] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:53:42,492] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:53:42,492] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1466ced-2906-4c61-8ae8-4d4c7a0afa64/dqc_reference
[2023-03-18 00:53:43,592] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:53:43,592] [INFO] Task started: Prodigal
[2023-03-18 00:53:43,592] [INFO] Running command: cat /var/lib/cwl/stg3a0a8df1-9f44-42de-8ee0-cdfdba838db9/OceanDNA-b1345.fa | prodigal -d OceanDNA-b1345/cds.fna -a OceanDNA-b1345/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:53:53,082] [INFO] Task succeeded: Prodigal
[2023-03-18 00:53:53,082] [INFO] Task started: HMMsearch
[2023-03-18 00:53:53,083] [INFO] Running command: hmmsearch --tblout OceanDNA-b1345/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1466ced-2906-4c61-8ae8-4d4c7a0afa64/dqc_reference/reference_markers.hmm OceanDNA-b1345/protein.faa > /dev/null
[2023-03-18 00:53:53,258] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:53:53,258] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3a0a8df1-9f44-42de-8ee0-cdfdba838db9/OceanDNA-b1345.fa]
[2023-03-18 00:53:53,276] [INFO] Query marker FASTA was written to OceanDNA-b1345/markers.fasta
[2023-03-18 00:53:53,276] [INFO] Task started: Blastn
[2023-03-18 00:53:53,276] [INFO] Running command: blastn -query OceanDNA-b1345/markers.fasta -db /var/lib/cwl/stgd1466ced-2906-4c61-8ae8-4d4c7a0afa64/dqc_reference/reference_markers.fasta -out OceanDNA-b1345/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:53:54,047] [INFO] Task succeeded: Blastn
[2023-03-18 00:53:54,048] [INFO] Selected 18 target genomes.
[2023-03-18 00:53:54,048] [INFO] Target genome list was writen to OceanDNA-b1345/target_genomes.txt
[2023-03-18 00:53:54,060] [INFO] Task started: fastANI
[2023-03-18 00:53:54,060] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a0a8df1-9f44-42de-8ee0-cdfdba838db9/OceanDNA-b1345.fa --refList OceanDNA-b1345/target_genomes.txt --output OceanDNA-b1345/fastani_result.tsv --threads 1
[2023-03-18 00:54:07,957] [INFO] Task succeeded: fastANI
[2023-03-18 00:54:07,957] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1466ced-2906-4c61-8ae8-4d4c7a0afa64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:54:07,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1466ced-2906-4c61-8ae8-4d4c7a0afa64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:54:07,966] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:54:07,966] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:54:07,966] [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
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	77.0195	125	391	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.8642	132	391	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.8147	86	391	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.9891	101	391	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.9177	90	391	95	below_threshold
Microbispora siamensis	strain=NBRC 104113	GCA_016863095.1	564413	564413	type	True	75.2853	78	391	95	below_threshold
Actinoplanes auranticolor	strain=NBRC 12245	GCA_018332655.1	47988	47988	type	True	75.2664	92	391	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	75.2275	56	391	95	below_threshold
Kibdelosporangium banguiense	strain=DSM 46670	GCA_017876405.1	1365924	1365924	type	True	75.194	54	391	95	below_threshold
Geodermatophilus telluris	strain=DSM 45421	GCA_900102745.1	1190417	1190417	type	True	75.1589	103	391	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	75.15	97	391	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	75.1039	85	391	95	below_threshold
Cellulomonas shaoxiangyii	strain=Z28	GCA_004798685.1	2566013	2566013	type	True	74.9292	69	391	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:54:07,966] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1345/tc_result.tsv
[2023-03-18 00:54:07,967] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:54:07,967] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:54:07,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1466ced-2906-4c61-8ae8-4d4c7a0afa64/dqc_reference/checkm_data
[2023-03-18 00:54:07,967] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:54:07,976] [INFO] Task started: CheckM
[2023-03-18 00:54:07,976] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1345/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1345/checkm_input OceanDNA-b1345/checkm_result
[2023-03-18 00:54:35,961] [INFO] Task succeeded: CheckM
[2023-03-18 00:54:35,961] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.85%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:54:36,007] [INFO] ===== Completeness check finished =====
[2023-03-18 00:54:36,007] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:54:36,007] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1345/markers.fasta)
[2023-03-18 00:54:36,008] [INFO] Task started: Blastn
[2023-03-18 00:54:36,008] [INFO] Running command: blastn -query OceanDNA-b1345/markers.fasta -db /var/lib/cwl/stgd1466ced-2906-4c61-8ae8-4d4c7a0afa64/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1345/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:54:37,187] [INFO] Task succeeded: Blastn
[2023-03-18 00:54:37,187] [INFO] Selected 15 target genomes.
[2023-03-18 00:54:37,188] [INFO] Target genome list was writen to OceanDNA-b1345/target_genomes_gtdb.txt
[2023-03-18 00:54:37,199] [INFO] Task started: fastANI
[2023-03-18 00:54:37,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a0a8df1-9f44-42de-8ee0-cdfdba838db9/OceanDNA-b1345.fa --refList OceanDNA-b1345/target_genomes_gtdb.txt --output OceanDNA-b1345/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:54:44,714] [INFO] Task succeeded: fastANI
[2023-03-18 00:54:44,721] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:54:44,722] [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_007118345.1	s__SKRR01 sp007118345	79.351	192	391	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SKRR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903941145.1	s__CAJANQ01 sp903941145	78.657	126	391	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAJANQ01	95.0	98.35	98.35	0.80	0.80	2	-
GCA_903868545.1	s__CAIPVR01 sp903868545	78.6348	166	391	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAIPVR01	95.0	99.51	99.50	0.87	0.86	3	-
GCA_003962875.1	s__AWTP1-35 sp003962875	78.5955	178	391	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__AWTP1-35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930035.1	s__CAJANQ01 sp903930035	78.3654	121	391	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAJANQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873135.1	s__SXMI01 sp903873135	77.9312	146	391	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	99.54	99.49	0.91	0.89	9	-
GCA_018268735.1	s__AWTP1-35 sp018268735	77.8736	100	391	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__AWTP1-35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005777415.1	s__SXMI01 sp005777415	77.3611	109	391	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	99.41	99.40	0.88	0.87	3	-
GCA_903925745.1	s__SXMI01 sp903925745	77.358	138	391	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019048865.1	s__Aquihabitans sp019048865	77.1794	142	391	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__Aquihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650215.1	s__Actinomarinicola tropica	76.8641	132	391	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	76.8129	130	391	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185275.1	s__JACPNX01 sp016185275	76.6017	115	391	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JACPNX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:54:44,722] [INFO] GTDB search result was written to OceanDNA-b1345/result_gtdb.tsv
[2023-03-18 00:54:44,722] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:54:44,727] [INFO] DFAST_QC result json was written to OceanDNA-b1345/dqc_result.json
[2023-03-18 00:54:44,727] [INFO] DFAST_QC completed!
[2023-03-18 00:54:44,727] [INFO] Total running time: 0h1m2s