[2023-03-17 02:57:06,473] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:57:06,473] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:57:06,473] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf4b276c-9846-4bc7-9f80-3d1f514cb18b/dqc_reference
[2023-03-17 02:57:08,636] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:57:08,637] [INFO] Task started: Prodigal
[2023-03-17 02:57:08,637] [INFO] Running command: cat /var/lib/cwl/stgd05d9bcc-3f5a-440b-9ac0-4cbeca040336/OceanDNA-b22660.fa | prodigal -d OceanDNA-b22660/cds.fna -a OceanDNA-b22660/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:57:28,196] [INFO] Task succeeded: Prodigal
[2023-03-17 02:57:28,197] [INFO] Task started: HMMsearch
[2023-03-17 02:57:28,197] [INFO] Running command: hmmsearch --tblout OceanDNA-b22660/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf4b276c-9846-4bc7-9f80-3d1f514cb18b/dqc_reference/reference_markers.hmm OceanDNA-b22660/protein.faa > /dev/null
[2023-03-17 02:57:28,384] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:57:28,385] [INFO] Found 6/6 markers.
[2023-03-17 02:57:28,402] [INFO] Query marker FASTA was written to OceanDNA-b22660/markers.fasta
[2023-03-17 02:57:28,404] [INFO] Task started: Blastn
[2023-03-17 02:57:28,404] [INFO] Running command: blastn -query OceanDNA-b22660/markers.fasta -db /var/lib/cwl/stgbf4b276c-9846-4bc7-9f80-3d1f514cb18b/dqc_reference/reference_markers.fasta -out OceanDNA-b22660/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:57:28,916] [INFO] Task succeeded: Blastn
[2023-03-17 02:57:28,917] [INFO] Selected 21 target genomes.
[2023-03-17 02:57:28,917] [INFO] Target genome list was writen to OceanDNA-b22660/target_genomes.txt
[2023-03-17 02:57:28,929] [INFO] Task started: fastANI
[2023-03-17 02:57:28,929] [INFO] Running command: fastANI --query /var/lib/cwl/stgd05d9bcc-3f5a-440b-9ac0-4cbeca040336/OceanDNA-b22660.fa --refList OceanDNA-b22660/target_genomes.txt --output OceanDNA-b22660/fastani_result.tsv --threads 1
[2023-03-17 02:57:46,631] [INFO] Task succeeded: fastANI
[2023-03-17 02:57:46,632] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf4b276c-9846-4bc7-9f80-3d1f514cb18b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:57:46,632] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf4b276c-9846-4bc7-9f80-3d1f514cb18b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:57:46,632] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:57:46,632] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:57:46,632] [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
--------------------------------------------------------------------------------
[2023-03-17 02:57:46,632] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22660/tc_result.tsv
[2023-03-17 02:57:46,633] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:57:46,633] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:57:46,633] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf4b276c-9846-4bc7-9f80-3d1f514cb18b/dqc_reference/checkm_data
[2023-03-17 02:57:46,637] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:57:46,641] [INFO] Task started: CheckM
[2023-03-17 02:57:46,641] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22660/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22660/checkm_input OceanDNA-b22660/checkm_result
[2023-03-17 02:58:36,234] [INFO] Task succeeded: CheckM
[2023-03-17 02:58:36,234] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:58:36,237] [INFO] ===== Completeness check finished =====
[2023-03-17 02:58:36,237] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:58:36,237] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22660/markers.fasta)
[2023-03-17 02:58:36,238] [INFO] Task started: Blastn
[2023-03-17 02:58:36,238] [INFO] Running command: blastn -query OceanDNA-b22660/markers.fasta -db /var/lib/cwl/stgbf4b276c-9846-4bc7-9f80-3d1f514cb18b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22660/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:58:37,062] [INFO] Task succeeded: Blastn
[2023-03-17 02:58:37,063] [INFO] Selected 22 target genomes.
[2023-03-17 02:58:37,063] [INFO] Target genome list was writen to OceanDNA-b22660/target_genomes_gtdb.txt
[2023-03-17 02:58:37,577] [INFO] Task started: fastANI
[2023-03-17 02:58:37,578] [INFO] Running command: fastANI --query /var/lib/cwl/stgd05d9bcc-3f5a-440b-9ac0-4cbeca040336/OceanDNA-b22660.fa --refList OceanDNA-b22660/target_genomes_gtdb.txt --output OceanDNA-b22660/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:58:51,734] [INFO] Task succeeded: fastANI
[2023-03-17 02:58:51,743] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:58:51,743] [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_002737405.1	s__BAIKAL-G1-2R sp002737405	97.6643	866	1004	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__BAIKAL-G1-2R	95.0	97.99	97.98	0.93	0.92	3	conclusive
GCA_903877395.1	s__BAIKAL-G1-2R sp903877395	81.1828	197	1004	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__BAIKAL-G1-2R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003670915.1	s__BAIKAL-G1-2R sp003670915	78.9475	126	1004	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__BAIKAL-G1-2R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903885565.1	s__CAISJI01 sp903885565	76.9605	144	1004	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__CAISJI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003670865.1	s__BAIKAL-G1-2R sp003670865	76.9146	144	1004	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__BAIKAL-G1-2R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970605.1	s__QWPN01 sp018970605	76.722	76	1004	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926295.1	s__RGVT01 sp009926295	76.4614	115	1004	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009924545.1	s__F1-20-MAGs016 sp009924545	76.4273	76	1004	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__F1-20-MAGs016	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903958265.1	s__QWPN01 sp903958265	76.3942	76	1004	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	98.26	98.26	0.80	0.80	2	-
GCA_903831155.1	s__QWPN01 sp903831155	76.3462	91	1004	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853835.1	s__QWPN01 sp017853835	76.2679	95	1004	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903949225.1	s__QWOP01 sp903949225	76.2393	67	1004	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005789975.1	s__QWPN01 sp005789975	76.1603	82	1004	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	99.49	99.44	0.83	0.81	3	-
GCA_005791575.1	s__F1-20-MAGs016 sp005791575	76.1346	72	1004	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__F1-20-MAGs016	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010027105.1	s__RGVT01 sp010027105	75.798	80	1004	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691925.1	s__QWOP01 sp009691925	75.7042	62	1004	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:58:51,744] [INFO] GTDB search result was written to OceanDNA-b22660/result_gtdb.tsv
[2023-03-17 02:58:51,744] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:58:51,745] [INFO] DFAST_QC result json was written to OceanDNA-b22660/dqc_result.json
[2023-03-17 02:58:51,745] [INFO] DFAST_QC completed!
[2023-03-17 02:58:51,745] [INFO] Total running time: 0h1m45s